About this document


All analyses were performed in R version 3.6.2. This is the code that accompanies the publication XXX. Here you will find all the code to repeat the statistical analyses performed in R and the figures created for the manuscript. The accompanying library preparation protocol and bioinformatic walkthrough can be found by clicking on the links.

If you have any issues or questions about the code please feel free to send an email to lexie.sturm@gmail.com.


Basic setup of R environment


Loading required packages

Make sure to set the working directory: setwd("~/path/to/directory/with/data")

setwd('../data')

For the following analyses we will require the use of multiple different R packages, we can use the package pacman to quickly load them.

if (!require("pacman")) install.packages("pacman")
pacman::p_load("adegenet", "dendextend", "flextable", "gdata", "ggdendro", "hierfstat", "Imap", "kableExtra", "paletteer", "patchwork", "officer", "poppr", "RColorBrewer", "reshape2", "StAMPP", "tidyverse", "vcfR", "vegan", "WGCNA", "boa", "plyr", "rgdal", "broom", "rgeos", "ggmap", "moments", "car", "multcompView", "lsmeans")

Figures and analyses

Sampling Map

 # set factors to false 
 options(stringsAsFactors = FALSE) 
 
 fknms <- readOGR("/Users/student/Documents/Florida\ Keys/Maps/fknms_py2/fknms_py.shp") 
## OGR data source with driver: ESRI Shapefile 
## Source: "/Users/student/Documents/Florida Keys/Maps/fknms_py2/fknms_py.shp", layer: "fknms_py"
## with 1 features
## It has 8 fields
 fknmsshpfile <- spTransform(fknms, "+init=epsg:4326") #WGS84 
 fknmsdta <- tidy(fknmsshpfile, group=group) 
## Regions defined for each Polygons
 #bathy<- readOGR("/Users/student/Documents/Florida\ Keys/Maps/tl_2016_12_cousub/tl_2016_12_cousub.shp") 
 #bathyshpfile <- spTransform(bathy, "+init=epsg:4326") #WGS84 
 #bathydta <- tidy(bathyshpfile, group=group) 
 
 fkSites = read.csv("sample-sites.csv", header=TRUE) 
 levels(fkSites$General.Site) 
## NULL
 fkSites$General.Site <- factor(fkSites$General.Site, levels = c("TER-South", "TER-North", "Lower-Keys", "Upper-Keys")) 
 
 baseMap <- get_stamenmap(bbox = c(left = -83, 
                                 bottom = 24, 
                                 right = -80, 
                                 top = 26), 
                        maptype = "terrain-background", 
                        crop = FALSE, 
                        zoom = 10) 
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 # plot map 
 levels(fkSites$General.Site) 
## [1] "TER-South"  "TER-North"  "Lower-Keys" "Upper-Keys"
 fkSites$General.Site = factor(fkSites$General.Site, levels(fkSites$General.Site)[c(1,3,2,4)]) 
 
 fkMap=ggmap(baseMap)+ 
   geom_polygon(aes(x=long, y=lat, group=group), 
                data=fknmsdta, 
                color="dark red", alpha=.2, size=.2) + 
   geom_point(data = fkSites, size= 3, aes(x = Lon, y = Lat, fill=General.Site, shape=Depth.Zone)) + 
   #scale_fill_manual(values = brewer.pal(name = "Set3", n = 4), name = "Population") + 
   scale_fill_paletteer_d("LaCroixColoR::PassionFruit", name= "Population", breaks=c("TER-South","TER-North","Lower-Keys", "Upper-Keys"), labels = c("DRTS", "DRTN", "LK", "UK"))+ 
   scale_shape_manual(values = c(24,25), name = "Depth Zone", breaks=c("Shallow", "Mesophotic")) + # define shape/color scales 
   scale_y_continuous(label=function(x){return(paste(x,"°N"))}, expand = c(0, 0))+ 
   scale_x_continuous(label=function(x){return(paste(-x,"°W"))}, expand = c(0, 0))+ 
   guides(fill = guide_legend(override.aes = list(shape = 21, size= 4)))+ 
   guides(shape = guide_legend(override.aes = list(size= 4)))+ 
   #labs(x="Longitude", y="Latitutde")+ 
   theme_bw()+ 
   theme(legend.position = "right", 
         axis.title.x = element_blank(), 
         axis.title.y = element_blank())+ 
   ggsn::scalebar(x.min = -83, 
                  y.min = 24, 
                  x.max = -80, 
                  y.max = 26, 
                  dist = 50, transform = TRUE, 
                  model = "WGS84", 
                 dist_unit="km", st.bottom=TRUE, st.dist=.03, st.size=3) 
## Scale for 'y' is already present. Adding another scale for 'y', which will replace
## the existing scale.
## Scale for 'x' is already present. Adding another scale for 'x', which will replace
## the existing scale.
 fkMap 

 ggsave("../figures/fkMap.tiff", plot=fkMap, height = 20, width = 25, unit = "cm", dpi = 300) 

Dendrogram with Clones

cloneBams = read.table("sampleList")[,1] # list of bam files
cloneMa = as.matrix(read.table("fkMcavClones.ibsMat")) # reads in IBS matrix produced by ANGSD
dimnames(cloneMa) = list(cloneBams,cloneBams)
clonesHc = hclust(as.dist(cloneMa),"ave")

cloneMeta = read.csv("inds2pops.csv") # list of bams files and their populations
clonePops = cloneMeta$pop
cloneDepth = cloneMeta$depth

cloneDend = cloneMa %>% as.dist() %>% hclust(.,"ave") %>% as.dendrogram()
cloneDData = cloneDend %>% dendro_data()

# Making the branches hang shorter so we can easily see clonal groups
cloneDData$segments$yend2 = cloneDData$segments$yend
for(i in 1:nrow(cloneDData$segments)) {
  if (cloneDData$segments$yend2[i] == 0) {
    cloneDData$segments$yend2[i] = (cloneDData$segments$y[i] - 0.03)}}

cloneDendPoints = cloneDData$labels
cloneDendPoints$pop = clonePops[order.dendrogram(cloneDend)]
cloneDendPoints$depth=cloneDepth[order.dendrogram(cloneDend)]
rownames(cloneDendPoints) = cloneDendPoints$label

# Making points at the leaves to place symbols for populations
point = as.vector(NA)
for(i in 1:nrow(cloneDData$segments)) {
  if (cloneDData$segments$yend[i] == 0) {
    point[i] = cloneDData$segments$y[i] - 0.03
  } else {
    point[i] = NA}}

cloneDendPoints$y = point[!is.na(point)]

techReps = c("009-1", "009-2", "009-3", "159-1", "159-2", "159-3", "171-1", "171-2", "171-3")

cloneDendPoints$depth=as.factor(cloneDendPoints$depth)
cloneDendPoints$depth = factor(cloneDendPoints$depth,levels(cloneDendPoints$depth)[c(2,1)])

cloneDendA = ggplot() +
  geom_segment(data = segment(cloneDData), aes(x = x, y = y, xend = xend, yend = yend2), size = 0.5) +
  geom_point(data = cloneDendPoints, aes(x = x, y = y, fill = pop, shape = depth), size = 4, stroke = 0.25) +
  #scale_fill_brewer(palette = "Dark2", name = "Population") +
  scale_fill_paletteer_d("LaCroixColoR::PassionFruit", breaks=c("TER-South","TER-North","Lower Keys", "Upper Keys"), name= "Population", labels = c("DRTS", "DRTN", "LK", "UK"))+
  scale_shape_manual(values=c(24, 25), breaks=c("Shallow","Mesophotic"), name="Depth Zone")+
  #geom_hline(yintercept = 0.1, color = "red", lty = 5, size = 0.75) + # creating a dashed line to indicate a clonal distance threshold
  geom_text(data = subset(cloneDendPoints, subset = label %in% techReps), aes(x = x, y = (y - .015), label = label), angle = 90) + # spacing technical replicates further from leaf
  geom_text(data = subset(cloneDendPoints, subset = !label %in% techReps), aes(x = x, y = (y - .010), label = label), angle = 90) +
  geom_text(data = subset(cloneDendPoints, subset = label %in% c("218", "223", "221", "226")), aes(x = (x + .5), y = (y - .018), label = "*"), angle = 90, size = 6) + # labeling natural clones with asterisks
  #coord_cartesian(xlim = c(3, 84)) +
  labs(y = "Genetic distance (1 - IBS)") +
  guides(fill = guide_legend(override.aes = list(shape = 21)))+
  theme_classic()

cloneDend = cloneDendA + theme(
  axis.title.x = element_blank(),
  axis.text.x = element_blank(),
  axis.line.x = element_blank(),
  axis.ticks.x = element_blank(),
  axis.title.y = element_text(size = 12, color = "black", angle = 90),
  axis.text.y = element_text(size = 10, color = "black"),
  axis.line.y = element_line(),
  axis.ticks.y = element_line(),
  panel.grid = element_blank(),
  panel.border = element_blank(),
  panel.background = element_blank(),
  plot.background = element_blank(),
  legend.key = element_blank(),
  legend.title = element_text(size = 12),
  legend.text = element_text(size = 10),
  legend.position = "left")

cloneDend

ggsave("../figures/cloneDend.tiff", plot = cloneDend, height = 4.75, width = 30, units = "in", dpi = 300)

Dendrogram no Clones

bamsNoClones = read.table("bamsNoClones")[,1] # list of bam file
snpMa = as.matrix(read.table("fkMcavNoClones.ibsMat"))
snpI2P = read.csv("inds2popsNoClones.csv") # 2-column tab-delimited table of individual assignments to populations; must be in the same order as samples in the bam list or vcf file.
row.names(snpI2P) = snpI2P[,1]

snpDend = snpMa %>% scale %>% dist %>%
  hclust %>% as.dendrogram

snpDData = dendro_data(snpDend)
snpDendPoints = snpDData$labels
snpDendPoints$site = snpI2P[,2][order.dendrogram(snpDend)]
snpDendPoints$depth = snpI2P[,3][order.dendrogram(snpDend)]

snpDendPoints$depth=as.factor(snpDendPoints$depth)
snpDendPoints$depth = factor(snpDendPoints$depth, levels(snpDendPoints$depth)[c(2,1)])

snpDendA = ggplot() +
  geom_segment(data = segment(snpDData), aes(x = x, y = y, xend = xend, yend = yend)) +
  geom_point(data = snpDendPoints, aes(x = x, y = y, fill = site, shape = depth), size = 5) +
  scale_shape_manual(values=c(24, 25), breaks=c("Shallow","Mesophotic"), name="Depth Zone")+
  scale_fill_paletteer_d("LaCroixColoR::PassionFruit", breaks=c("TER-South","TER-North","Lower Keys", "Upper Keys"), name= "Population", labels = c("DRTS", "DRTN", "LK", "UK"))+
  guides(fill = guide_legend(override.aes = list(shape = 21)))+
  theme_dendro()

snpDend = snpDendA + theme(
  legend.key = element_blank(),
  legend.title = element_text(size = 14),
  legend.text = element_text(size = 12))

snpDend

ggsave("../figures/snpDend.tiff", plot = snpDend, height = 4.75, width = 35, units = "in", dpi = 300)

Heterozygosity

hetero=read.csv("sampleHeterozygosity.csv")
heteroStatAllSites <- ddply(hetero, c("popdepth"), summarise,
               N    = length(HeterozygosityAllSites),
               mean = mean(HeterozygosityAllSites),
               sd   = sd(HeterozygosityAllSites),
               se   = sd / sqrt(N))
max(heteroStatAllSites$mean, na.rm = TRUE)
## [1] 0.002648148
min(heteroStatAllSites$mean, na.rm = TRUE)
## [1] 0.002378125
heteroVariantSites <- ddply(hetero, c("popdepth"), summarise,
               N    = length(HeterozygosityVariantSites),
               mean = mean(HeterozygosityVariantSites),
               sd   = sd(HeterozygosityVariantSites),
               se   = sd / sqrt(N))
max(heteroVariantSites$mean, na.rm = TRUE)
## [1] 0.2547852
min(heteroVariantSites$mean, na.rm = TRUE)
## [1] 0.2206937
heteroPlot <- ggplot(hetero, aes(x=popdepth, y=HeterozygosityAllSites)) + 
  geom_boxplot()+
  theme_bw()
heteroPlot

## PCoA with IBS

snpMa = as.matrix(read.table("fkMcavNoClones.ibsMat"))
fkMds = cmdscale(snpMa, eig = TRUE, x.ret = TRUE)

# Determine percent variation captured on each axis
# Calculate the eigenvalues so later we can figure out % variation shown on each Principal Coordinate
fkSnpPcoaVar = round(fkMds$eig/sum(fkMds$eig)*100, 1)
fkSnpPcoaVar
##   [1] 12.7  3.8  2.2  2.1  1.9  1.0  0.8  0.8  0.8  0.8  0.7  0.7  0.7  0.7  0.7  0.7
##  [17]  0.7  0.7  0.7  0.7  0.7  0.6  0.6  0.6  0.6  0.6  0.6  0.6  0.6  0.6  0.6  0.6
##  [33]  0.6  0.6  0.6  0.6  0.6  0.6  0.6  0.6  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5
##  [49]  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5
##  [65]  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4
##  [81]  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4
##  [97]  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.4  0.3
## [113]  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3
## [129]  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3
## [145]  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.3  0.2  0.2  0.2  0.2  0.2  0.2
## [161]  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2
## [177]  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.1
## [193]  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1  0.1
## [209]  0.1  0.1  0.0  0.0  0.0  0.0  0.0
# Format data to plot
fkSnpPcoaValues = fkMds$points
fkSnpPcoaValues
##                [,1]           [,2]
##   [1,] -0.023138161  0.03227476909
##   [2,] -0.058735739 -0.00204461610
##   [3,] -0.059088863 -0.00139960752
##   [4,] -0.063337537  0.00712084220
##   [5,] -0.063284280  0.00551861577
##   [6,] -0.071593487  0.00485001928
##   [7,]  0.075618706 -0.05442781813
##   [8,] -0.071465199 -0.00353248771
##   [9,] -0.069434766 -0.00023634101
##  [10,]  0.073631471 -0.04890491914
##  [11,]  0.068266136 -0.04480272940
##  [12,]  0.073677298 -0.05630736518
##  [13,]  0.045992042 -0.01004671318
##  [14,]  0.056368086 -0.03070560128
##  [15,]  0.048263228  0.02431332960
##  [16,]  0.071661406 -0.05784332383
##  [17,]  0.058769926 -0.01250926439
##  [18,] -0.016648062  0.01638740112
##  [19,]  0.088153905  0.08641075198
##  [20,]  0.063328988  0.03675465175
##  [21,]  0.050598373 -0.01068518486
##  [22,]  0.076142699 -0.05195136115
##  [23,]  0.084355002  0.06915354665
##  [24,] -0.055074456  0.00278656209
##  [25,]  0.074320706 -0.05718969428
##  [26,]  0.071502013 -0.04915155757
##  [27,]  0.045517786 -0.01030571632
##  [28,] -0.055925363  0.00047639521
##  [29,] -0.066526158  0.00599217579
##  [30,]  0.074680008 -0.05698660894
##  [31,]  0.063396291 -0.05589119681
##  [32,]  0.078581834 -0.04259874763
##  [33,] -0.056844813 -0.00505055668
##  [34,]  0.024813502  0.04772197577
##  [35,] -0.058951790  0.00213259100
##  [36,]  0.072440838 -0.05643520028
##  [37,]  0.083145657  0.06913823760
##  [38,]  0.027241737  0.04580286065
##  [39,]  0.071154823 -0.04930723312
##  [40,]  0.072468953 -0.05685814222
##  [41,]  0.070094080 -0.05317212377
##  [42,] -0.069011064 -0.00206107710
##  [43,] -0.060959780 -0.00966661140
##  [44,]  0.048565989 -0.00619631667
##  [45,] -0.013767986 -0.00898246395
##  [46,] -0.075860400 -0.01017456790
##  [47,]  0.068705807 -0.05160557873
##  [48,] -0.074232889 -0.00468048127
##  [49,] -0.072576347  0.00050623463
##  [50,] -0.069206209 -0.00183976634
##  [51,] -0.064068726 -0.00024945959
##  [52,] -0.070852014 -0.00529917237
##  [53,] -0.072237315 -0.00631612830
##  [54,]  0.064922546 -0.02859881389
##  [55,] -0.060213172 -0.00103197872
##  [56,] -0.072194119  0.00295350527
##  [57,] -0.070103403 -0.00644396245
##  [58,] -0.063281603  0.00010877405
##  [59,] -0.072292609 -0.00358586277
##  [60,] -0.064239017  0.00877308969
##  [61,] -0.063004492 -0.00791334893
##  [62,] -0.073083290 -0.00444825166
##  [63,] -0.071660119  0.00203244948
##  [64,]  0.081905887  0.06831994371
##  [65,] -0.069926040  0.00237284390
##  [66,] -0.065915225  0.00240162283
##  [67,]  0.082099685  0.07404893567
##  [68,]  0.070486523 -0.04558279757
##  [69,] -0.060991431  0.00248332660
##  [70,]  0.077150442  0.06702861867
##  [71,]  0.079283885  0.07118839050
##  [72,]  0.082808031  0.07140828153
##  [73,]  0.044457580 -0.00699843498
##  [74,]  0.061238116  0.03192522369
##  [75,]  0.038689620  0.02010582744
##  [76,]  0.048684105 -0.00943213787
##  [77,]  0.072463426 -0.04739791107
##  [78,]  0.084774954  0.07406410914
##  [79,]  0.070294740  0.01820359354
##  [80,]  0.067930308  0.03130991289
##  [81,]  0.071496522  0.06651595138
##  [82,]  0.034850958 -0.00716926664
##  [83,]  0.059581765 -0.03850909688
##  [84,]  0.044081250 -0.01189334701
##  [85,]  0.079424441  0.07067161673
##  [86,]  0.072611807 -0.05075728456
##  [87,]  0.081454604 -0.05048527036
##  [88,]  0.049460092 -0.01252826310
##  [89,]  0.070986609 -0.05051605199
##  [90,]  0.066867355  0.02512797785
##  [91,]  0.039290775 -0.01122253577
##  [92,]  0.085909622  0.06126923057
##  [93,]  0.042750275 -0.01256979025
##  [94,]  0.070326866 -0.04977825786
##  [95,] -0.073928582 -0.00290790049
##  [96,] -0.083687129 -0.00114950021
##  [97,] -0.061788686  0.00288677097
##  [98,] -0.072453685  0.00667061728
##  [99,]  0.074963474  0.07243867262
## [100,] -0.059599053  0.00308422965
## [101,] -0.058197301  0.00123046692
## [102,]  0.072188045  0.06652194118
## [103,] -0.051677121 -0.01013612455
## [104,] -0.073814864 -0.00371997317
## [105,]  0.061854778  0.06207926416
## [106,]  0.076447424 -0.04691294568
## [107,]  0.078379278  0.07812339057
## [108,]  0.050808059 -0.01274628529
## [109,]  0.075320468 -0.04949966609
## [110,] -0.065119718  0.00639202816
## [111,] -0.043114729  0.01224750718
## [112,] -0.056563129 -0.00114501952
## [113,] -0.062633621  0.01017546646
## [114,] -0.053825058  0.00598441083
## [115,] -0.071637561 -0.00191919907
## [116,]  0.069569516 -0.04708464365
## [117,]  0.044800517 -0.01028870933
## [118,]  0.074316226 -0.04965978656
## [119,]  0.076933592 -0.05307827568
## [120,]  0.051458214 -0.01494565776
## [121,]  0.086334803  0.07570218718
## [122,]  0.081044013  0.06498443665
## [123,]  0.079301084 -0.04968535720
## [124,]  0.080332433 -0.05726006661
## [125,]  0.079772520 -0.04896981269
## [126,]  0.081196334  0.07284377054
## [127,]  0.084012457  0.06319981843
## [128,]  0.077390936 -0.05255602411
## [129,]  0.047317556 -0.00831358827
## [130,]  0.069205109 -0.04332882063
## [131,]  0.082287827  0.07583528554
## [132,]  0.074585935 -0.05279525510
## [133,] -0.057804491 -0.00178429501
## [134,]  0.081350260  0.06466528163
## [135,] -0.057630152  0.00007746181
## [136,]  0.083897107  0.06698838425
## [137,]  0.075928002 -0.05271917183
## [138,]  0.070842180 -0.04866969227
## [139,]  0.080851307  0.07666324290
## [140,]  0.077435306 -0.04985581677
## [141,]  0.043306080 -0.02804582126
## [142,]  0.081845542  0.07161907700
## [143,]  0.072369910 -0.05355120663
## [144,] -0.070165003  0.00226958134
## [145,]  0.023829885  0.05322109979
## [146,] -0.064939826  0.00689326946
## [147,] -0.067770153  0.00528354744
## [148,] -0.058707279  0.01011508079
## [149,] -0.059091081  0.00741932530
## [150,] -0.058009087  0.00192451175
## [151,] -0.057222379  0.00076726064
## [152,] -0.061870658  0.00460142520
## [153,]  0.085883023  0.07056459648
## [154,] -0.063743742  0.00714257612
## [155,]  0.026014517  0.04878855057
## [156,] -0.063944119  0.00085820495
## [157,] -0.073606246 -0.00233707820
## [158,]  0.077664205 -0.05387708935
## [159,] -0.070614864  0.00044266874
## [160,] -0.076357931 -0.00259570195
## [161,] -0.058106135 -0.00280014551
## [162,] -0.061546000  0.00425454617
## [163,] -0.072883709 -0.00668950440
## [164,] -0.074867544 -0.00028121178
## [165,] -0.066473947  0.00316370530
## [166,]  0.077729675 -0.04749865097
## [167,] -0.064486642  0.00484439669
## [168,] -0.075375761 -0.00514513505
## [169,] -0.056239723  0.00562190140
## [170,] -0.062195507 -0.00085989685
## [171,] -0.069452269 -0.00700825096
## [172,]  0.073510974 -0.05662725102
## [173,] -0.065872212 -0.01107917735
## [174,] -0.061845615  0.00186170627
## [175,] -0.054032355  0.00172600273
## [176,] -0.059565700 -0.00269777656
## [177,]  0.070479395 -0.05517039547
## [178,] -0.050014071  0.00492170437
## [179,] -0.063278974 -0.00548824116
## [180,] -0.060546897  0.00331955948
## [181,] -0.064893565  0.00778244463
## [182,] -0.067524623 -0.01045769684
## [183,]  0.052463511 -0.05392050791
## [184,] -0.059712547  0.00313895108
## [185,] -0.077968329 -0.00215460077
## [186,] -0.071170641  0.00133733698
## [187,] -0.067110448 -0.00086554900
## [188,] -0.002852639 -0.03167166008
## [189,] -0.063196756  0.00521096495
## [190,]  0.003421594 -0.01556319053
## [191,] -0.046979927 -0.00305041903
## [192,] -0.065258181  0.00294638421
## [193,] -0.016955065 -0.02061242048
## [194,] -0.065777711 -0.00234690448
## [195,]  0.059578722  0.06163882428
## [196,]  0.048721852 -0.00442204082
## [197,] -0.064179159 -0.00003529347
## [198,] -0.071377029 -0.00438152639
## [199,] -0.068693656 -0.00181282943
## [200,] -0.074792005 -0.00403227742
## [201,]  0.024190252  0.05709267937
## [202,] -0.063284821  0.00195765540
## [203,] -0.067763657  0.00898885427
## [204,] -0.066022674 -0.00438777936
## [205,] -0.063271172 -0.00037414791
## [206,] -0.071794568 -0.00534499324
## [207,]  0.030634903  0.05235783277
## [208,] -0.077159133 -0.00732436888
## [209,] -0.072703242 -0.00703501858
## [210,]  0.022621692  0.04855444502
## [211,]  0.024225550  0.04568635764
## [212,] -0.063499916  0.00218060829
## [213,] -0.075537320  0.00067007824
## [214,] -0.064593148  0.00081026672
## [215,] -0.076257950 -0.00547105691
snpI2P = read.csv("inds2popsNoClones.csv") # 2-column tab-delimited table of individual assignments to populations; must be in the same order as samples in the bam list or vcf file.
row.names(snpI2P) = snpI2P[,1]
fkSnpPcoaValues=cbind(snpI2P, fkSnpPcoaValues)
fkSnpPcoaValues =as.data.frame(fkSnpPcoaValues, sample = rownames(fkSnpPcoaValues))
colnames(fkSnpPcoaValues)[5] <- "PCo1"
colnames(fkSnpPcoaValues)[6] <- "PCo2"
fkSnpPcoaValues
##     sample        pop      depth               popsite         PCo1           PCo2
## 2        2  TER-North Mesophotic  TER-North-Mesophotic -0.023138161  0.03227476909
## 4        4  TER-North Mesophotic  TER-North-Mesophotic -0.058735739 -0.00204461610
## 5        5  TER-North Mesophotic  TER-North-Mesophotic -0.059088863 -0.00139960752
## 6        6  TER-North Mesophotic  TER-North-Mesophotic -0.063337537  0.00712084220
## 7        7  TER-North Mesophotic  TER-North-Mesophotic -0.063284280  0.00551861577
## 8        8  TER-North Mesophotic  TER-North-Mesophotic -0.071593487  0.00485001928
## 9        9  TER-North Mesophotic  TER-North-Mesophotic  0.075618706 -0.05442781813
## 10      10  TER-North Mesophotic  TER-North-Mesophotic -0.071465199 -0.00353248771
## 12      12  TER-North Mesophotic  TER-North-Mesophotic -0.069434766 -0.00023634101
## 13      13  TER-North Mesophotic  TER-North-Mesophotic  0.073631471 -0.04890491914
## 14      14  TER-North    Shallow     TER-North-Shallow  0.068266136 -0.04480272940
## 15      15  TER-North    Shallow     TER-North-Shallow  0.073677298 -0.05630736518
## 16      16  TER-North    Shallow     TER-North-Shallow  0.045992042 -0.01004671318
## 17      17  TER-North    Shallow     TER-North-Shallow  0.056368086 -0.03070560128
## 18      18  TER-North    Shallow     TER-North-Shallow  0.048263228  0.02431332960
## 19      19  TER-North    Shallow     TER-North-Shallow  0.071661406 -0.05784332383
## 20      20  TER-North    Shallow     TER-North-Shallow  0.058769926 -0.01250926439
## 21      21  TER-North    Shallow     TER-North-Shallow -0.016648062  0.01638740112
## 22      22  TER-North    Shallow     TER-North-Shallow  0.088153905  0.08641075198
## 23      23  TER-North    Shallow     TER-North-Shallow  0.063328988  0.03675465175
## 24      24  TER-North    Shallow     TER-North-Shallow  0.050598373 -0.01068518486
## 26      26  TER-North    Shallow     TER-North-Shallow  0.076142699 -0.05195136115
## 27      27  TER-North    Shallow     TER-North-Shallow  0.084355002  0.06915354665
## 28      28  TER-North    Shallow     TER-North-Shallow -0.055074456  0.00278656209
## 29      29  TER-North    Shallow     TER-North-Shallow  0.074320706 -0.05718969428
## 30      30  TER-North    Shallow     TER-North-Shallow  0.071502013 -0.04915155757
## 31      31  TER-North    Shallow     TER-North-Shallow  0.045517786 -0.01030571632
## 32      32  TER-North    Shallow     TER-North-Shallow -0.055925363  0.00047639521
## 33      33  TER-North    Shallow     TER-North-Shallow -0.066526158  0.00599217579
## 34      34  TER-North    Shallow     TER-North-Shallow  0.074680008 -0.05698660894
## 36      36  TER-North    Shallow     TER-North-Shallow  0.063396291 -0.05589119681
## 37      37  TER-North Mesophotic  TER-North-Mesophotic  0.078581834 -0.04259874763
## 38      38  TER-North Mesophotic  TER-North-Mesophotic -0.056844813 -0.00505055668
## 39      39  TER-North Mesophotic  TER-North-Mesophotic  0.024813502  0.04772197577
## 40      40  TER-North Mesophotic  TER-North-Mesophotic -0.058951790  0.00213259100
## 41      41  TER-North Mesophotic  TER-North-Mesophotic  0.072440838 -0.05643520028
## 42      42  TER-North Mesophotic  TER-North-Mesophotic  0.083145657  0.06913823760
## 44      44  TER-North Mesophotic  TER-North-Mesophotic  0.027241737  0.04580286065
## 45      45  TER-North Mesophotic  TER-North-Mesophotic  0.071154823 -0.04930723312
## 46      46  TER-North Mesophotic  TER-North-Mesophotic  0.072468953 -0.05685814222
## 47      47  TER-North Mesophotic  TER-North-Mesophotic  0.070094080 -0.05317212377
## 48      48  TER-North    Shallow     TER-North-Shallow -0.069011064 -0.00206107710
## 49      49  TER-North    Shallow     TER-North-Shallow -0.060959780 -0.00966661140
## 50      50  TER-North    Shallow     TER-North-Shallow  0.048565989 -0.00619631667
## 52      52  TER-North    Shallow     TER-North-Shallow -0.013767986 -0.00898246395
## 53      53  TER-North    Shallow     TER-North-Shallow -0.075860400 -0.01017456790
## 54      54  TER-North Mesophotic  TER-North-Mesophotic  0.068705807 -0.05160557873
## 55      55  TER-North Mesophotic  TER-North-Mesophotic -0.074232889 -0.00468048127
## 56      56  TER-North Mesophotic  TER-North-Mesophotic -0.072576347  0.00050623463
## 60      60  TER-North    Shallow     TER-North-Shallow -0.069206209 -0.00183976634
## 61      61  TER-South Mesophotic  TER-South-Mesophotic -0.064068726 -0.00024945959
## 62      62  TER-South Mesophotic  TER-South-Mesophotic -0.070852014 -0.00529917237
## 63      63  TER-South Mesophotic  TER-South-Mesophotic -0.072237315 -0.00631612830
## 64      64  TER-South Mesophotic  TER-South-Mesophotic  0.064922546 -0.02859881389
## 65      65  TER-South Mesophotic  TER-South-Mesophotic -0.060213172 -0.00103197872
## 66      66  TER-South Mesophotic  TER-South-Mesophotic -0.072194119  0.00295350527
## 67      67  TER-South Mesophotic  TER-South-Mesophotic -0.070103403 -0.00644396245
## 68      68  TER-South Mesophotic  TER-South-Mesophotic -0.063281603  0.00010877405
## 69      69  TER-South Mesophotic  TER-South-Mesophotic -0.072292609 -0.00358586277
## 70      70  TER-South Mesophotic  TER-South-Mesophotic -0.064239017  0.00877308969
## 71      71  TER-South Mesophotic  TER-South-Mesophotic -0.063004492 -0.00791334893
## 72      72  TER-South Mesophotic  TER-South-Mesophotic -0.073083290 -0.00444825166
## 73      73  TER-South Mesophotic  TER-South-Mesophotic -0.071660119  0.00203244948
## 74      74  TER-South Mesophotic  TER-South-Mesophotic  0.081905887  0.06831994371
## 75      75  TER-South Mesophotic  TER-South-Mesophotic -0.069926040  0.00237284390
## 76      76  TER-South Mesophotic  TER-South-Mesophotic -0.065915225  0.00240162283
## 77      77  TER-South Mesophotic  TER-South-Mesophotic  0.082099685  0.07404893567
## 78      78  TER-South Mesophotic  TER-South-Mesophotic  0.070486523 -0.04558279757
## 79      79  TER-South Mesophotic  TER-South-Mesophotic -0.060991431  0.00248332660
## 80      80  TER-South Mesophotic  TER-South-Mesophotic  0.077150442  0.06702861867
## 82      82  TER-South    Shallow     TER-South-Shallow  0.079283885  0.07118839050
## 84      84  TER-South    Shallow     TER-South-Shallow  0.082808031  0.07140828153
## 85      85  TER-South    Shallow     TER-South-Shallow  0.044457580 -0.00699843498
## 86      86  TER-South    Shallow     TER-South-Shallow  0.061238116  0.03192522369
## 87      87  TER-South    Shallow     TER-South-Shallow  0.038689620  0.02010582744
## 88      88  TER-South    Shallow     TER-South-Shallow  0.048684105 -0.00943213787
## 89      89  TER-South    Shallow     TER-South-Shallow  0.072463426 -0.04739791107
## 90      90  TER-South    Shallow     TER-South-Shallow  0.084774954  0.07406410914
## 91      91  TER-South    Shallow     TER-South-Shallow  0.070294740  0.01820359354
## 92      92  TER-South    Shallow     TER-South-Shallow  0.067930308  0.03130991289
## 93      93  TER-South    Shallow     TER-South-Shallow  0.071496522  0.06651595138
## 94      94  TER-South    Shallow     TER-South-Shallow  0.034850958 -0.00716926664
## 95      95  TER-South    Shallow     TER-South-Shallow  0.059581765 -0.03850909688
## 96      96  TER-South    Shallow     TER-South-Shallow  0.044081250 -0.01189334701
## 97      97  TER-South    Shallow     TER-South-Shallow  0.079424441  0.07067161673
## 98      98  TER-South    Shallow     TER-South-Shallow  0.072611807 -0.05075728456
## 99      99  TER-South    Shallow     TER-South-Shallow  0.081454604 -0.05048527036
## 100    100  TER-South    Shallow     TER-South-Shallow  0.049460092 -0.01252826310
## 101    101  TER-South    Shallow     TER-South-Shallow  0.070986609 -0.05051605199
## 102    102  TER-South    Shallow     TER-South-Shallow  0.066867355  0.02512797785
## 103    103  TER-South    Shallow     TER-South-Shallow  0.039290775 -0.01122253577
## 104    104  TER-South    Shallow     TER-South-Shallow  0.085909622  0.06126923057
## 105    105  TER-South    Shallow     TER-South-Shallow  0.042750275 -0.01256979025
## 106    106  TER-South    Shallow     TER-South-Shallow  0.070326866 -0.04977825786
## 107    107  TER-South Mesophotic  TER-South-Mesophotic -0.073928582 -0.00290790049
## 108    108  TER-South Mesophotic  TER-South-Mesophotic -0.083687129 -0.00114950021
## 109    109  TER-South Mesophotic  TER-South-Mesophotic -0.061788686  0.00288677097
## 110    110  TER-South Mesophotic  TER-South-Mesophotic -0.072453685  0.00667061728
## 111    111  TER-South Mesophotic  TER-South-Mesophotic  0.074963474  0.07243867262
## 112    112  TER-South Mesophotic  TER-South-Mesophotic -0.059599053  0.00308422965
## 113    113  TER-South Mesophotic  TER-South-Mesophotic -0.058197301  0.00123046692
## 114    114  TER-South Mesophotic  TER-South-Mesophotic  0.072188045  0.06652194118
## 115    115  TER-South Mesophotic  TER-South-Mesophotic -0.051677121 -0.01013612455
## 116    116  TER-South Mesophotic  TER-South-Mesophotic -0.073814864 -0.00371997317
## 117    117  TER-South Mesophotic  TER-South-Mesophotic  0.061854778  0.06207926416
## 118    118  TER-South    Shallow     TER-South-Shallow  0.076447424 -0.04691294568
## 119    119  TER-South    Shallow     TER-South-Shallow  0.078379278  0.07812339057
## 120    120  TER-South    Shallow     TER-South-Shallow  0.050808059 -0.01274628529
## 121    121  TER-South    Shallow     TER-South-Shallow  0.075320468 -0.04949966609
## 122    122  TER-South Mesophotic  TER-South-Mesophotic -0.065119718  0.00639202816
## 123    123  TER-South Mesophotic  TER-South-Mesophotic -0.043114729  0.01224750718
## 124    124  TER-South Mesophotic  TER-South-Mesophotic -0.056563129 -0.00114501952
## 125    125  TER-South Mesophotic  TER-South-Mesophotic -0.062633621  0.01017546646
## 126    126  TER-South Mesophotic  TER-South-Mesophotic -0.053825058  0.00598441083
## 127    127  TER-South Mesophotic  TER-South-Mesophotic -0.071637561 -0.00191919907
## 128    128 Lower Keys    Shallow    Lower Keys-Shallow  0.069569516 -0.04708464365
## 129    129 Lower Keys    Shallow    Lower Keys-Shallow  0.044800517 -0.01028870933
## 130    130 Lower Keys    Shallow    Lower Keys-Shallow  0.074316226 -0.04965978656
## 131    131 Lower Keys    Shallow    Lower Keys-Shallow  0.076933592 -0.05307827568
## 132    132 Lower Keys    Shallow    Lower Keys-Shallow  0.051458214 -0.01494565776
## 133    133 Lower Keys    Shallow    Lower Keys-Shallow  0.086334803  0.07570218718
## 134    134 Lower Keys    Shallow    Lower Keys-Shallow  0.081044013  0.06498443665
## 135    135 Lower Keys    Shallow    Lower Keys-Shallow  0.079301084 -0.04968535720
## 136    136 Lower Keys    Shallow    Lower Keys-Shallow  0.080332433 -0.05726006661
## 137    137 Lower Keys    Shallow    Lower Keys-Shallow  0.079772520 -0.04896981269
## 138    138 Lower Keys    Shallow    Lower Keys-Shallow  0.081196334  0.07284377054
## 139    139 Lower Keys    Shallow    Lower Keys-Shallow  0.084012457  0.06319981843
## 140    140 Lower Keys    Shallow    Lower Keys-Shallow  0.077390936 -0.05255602411
## 141    141 Lower Keys    Shallow    Lower Keys-Shallow  0.047317556 -0.00831358827
## 142    142 Lower Keys    Shallow    Lower Keys-Shallow  0.069205109 -0.04332882063
## 143    143 Lower Keys    Shallow    Lower Keys-Shallow  0.082287827  0.07583528554
## 144    144 Lower Keys    Shallow    Lower Keys-Shallow  0.074585935 -0.05279525510
## 145    145 Lower Keys    Shallow    Lower Keys-Shallow -0.057804491 -0.00178429501
## 146    146 Lower Keys    Shallow    Lower Keys-Shallow  0.081350260  0.06466528163
## 147    147 Lower Keys    Shallow    Lower Keys-Shallow -0.057630152  0.00007746181
## 148    148 Lower Keys    Shallow    Lower Keys-Shallow  0.083897107  0.06698838425
## 149    149 Lower Keys    Shallow    Lower Keys-Shallow  0.075928002 -0.05271917183
## 150    150 Lower Keys    Shallow    Lower Keys-Shallow  0.070842180 -0.04866969227
## 151    151 Lower Keys    Shallow    Lower Keys-Shallow  0.080851307  0.07666324290
## 152    152 Lower Keys    Shallow    Lower Keys-Shallow  0.077435306 -0.04985581677
## 153    153 Lower Keys    Shallow    Lower Keys-Shallow  0.043306080 -0.02804582126
## 154    154 Lower Keys    Shallow    Lower Keys-Shallow  0.081845542  0.07161907700
## 155    155 Lower Keys    Shallow    Lower Keys-Shallow  0.072369910 -0.05355120663
## 156    156 Lower Keys    Shallow    Lower Keys-Shallow -0.070165003  0.00226958134
## 157    157 Lower Keys Mesophotic Lower Keys-Mesophotic  0.023829885  0.05322109979
## 158    158 Lower Keys Mesophotic Lower Keys-Mesophotic -0.064939826  0.00689326946
## 159    159 Lower Keys Mesophotic Lower Keys-Mesophotic -0.067770153  0.00528354744
## 160    160 Lower Keys Mesophotic Lower Keys-Mesophotic -0.058707279  0.01011508079
## 161    161 Lower Keys Mesophotic Lower Keys-Mesophotic -0.059091081  0.00741932530
## 162    162 Lower Keys Mesophotic Lower Keys-Mesophotic -0.058009087  0.00192451175
## 163    163 Lower Keys Mesophotic Lower Keys-Mesophotic -0.057222379  0.00076726064
## 164    164 Lower Keys Mesophotic Lower Keys-Mesophotic -0.061870658  0.00460142520
## 165    165 Lower Keys Mesophotic Lower Keys-Mesophotic  0.085883023  0.07056459648
## 166    166 Lower Keys Mesophotic Lower Keys-Mesophotic -0.063743742  0.00714257612
## 167    167 Lower Keys Mesophotic Lower Keys-Mesophotic  0.026014517  0.04878855057
## 168    168 Lower Keys Mesophotic Lower Keys-Mesophotic -0.063944119  0.00085820495
## 169    169 Lower Keys Mesophotic Lower Keys-Mesophotic -0.073606246 -0.00233707820
## 170    170 Lower Keys    Shallow    Lower Keys-Shallow  0.077664205 -0.05387708935
## 171    171 Upper Keys Mesophotic Upper Keys-Mesophotic -0.070614864  0.00044266874
## 172    172 Upper Keys Mesophotic Upper Keys-Mesophotic -0.076357931 -0.00259570195
## 173    173 Upper Keys Mesophotic Upper Keys-Mesophotic -0.058106135 -0.00280014551
## 174    174 Upper Keys Mesophotic Upper Keys-Mesophotic -0.061546000  0.00425454617
## 175    175 Upper Keys Mesophotic Upper Keys-Mesophotic -0.072883709 -0.00668950440
## 176    176 Upper Keys Mesophotic Upper Keys-Mesophotic -0.074867544 -0.00028121178
## 177    177 Upper Keys Mesophotic Upper Keys-Mesophotic -0.066473947  0.00316370530
## 178    178 Upper Keys Mesophotic Upper Keys-Mesophotic  0.077729675 -0.04749865097
## 179    179 Upper Keys    Shallow    Upper Keys-Shallow -0.064486642  0.00484439669
## 180    180 Upper Keys    Shallow    Upper Keys-Shallow -0.075375761 -0.00514513505
## 181    181 Upper Keys    Shallow    Upper Keys-Shallow -0.056239723  0.00562190140
## 182    182 Upper Keys    Shallow    Upper Keys-Shallow -0.062195507 -0.00085989685
## 183    183 Upper Keys    Shallow    Upper Keys-Shallow -0.069452269 -0.00700825096
## 184    184 Upper Keys    Shallow    Upper Keys-Shallow  0.073510974 -0.05662725102
## 185    185 Upper Keys    Shallow    Upper Keys-Shallow -0.065872212 -0.01107917735
## 186    186 Upper Keys    Shallow    Upper Keys-Shallow -0.061845615  0.00186170627
## 187    187 Upper Keys Mesophotic Upper Keys-Mesophotic -0.054032355  0.00172600273
## 188    188 Upper Keys Mesophotic Upper Keys-Mesophotic -0.059565700 -0.00269777656
## 189    189 Upper Keys Mesophotic Upper Keys-Mesophotic  0.070479395 -0.05517039547
## 190    190 Upper Keys Mesophotic Upper Keys-Mesophotic -0.050014071  0.00492170437
## 191    191 Upper Keys Mesophotic Upper Keys-Mesophotic -0.063278974 -0.00548824116
## 192    192 Upper Keys Mesophotic Upper Keys-Mesophotic -0.060546897  0.00331955948
## 193    193 Upper Keys Mesophotic Upper Keys-Mesophotic -0.064893565  0.00778244463
## 194    194 Upper Keys    Shallow    Upper Keys-Shallow -0.067524623 -0.01045769684
## 195    195 Upper Keys    Shallow    Upper Keys-Shallow  0.052463511 -0.05392050791
## 196    196 Upper Keys    Shallow    Upper Keys-Shallow -0.059712547  0.00313895108
## 198    198 Upper Keys    Shallow    Upper Keys-Shallow -0.077968329 -0.00215460077
## 199    199 Upper Keys    Shallow    Upper Keys-Shallow -0.071170641  0.00133733698
## 200    200 Upper Keys    Shallow    Upper Keys-Shallow -0.067110448 -0.00086554900
## 201    201 Upper Keys Mesophotic Upper Keys-Mesophotic -0.002852639 -0.03167166008
## 202    202 Upper Keys Mesophotic Upper Keys-Mesophotic -0.063196756  0.00521096495
## 205    205 Upper Keys Mesophotic Upper Keys-Mesophotic  0.003421594 -0.01556319053
## 208    208 Upper Keys Mesophotic Upper Keys-Mesophotic -0.046979927 -0.00305041903
## 209    209 Upper Keys Mesophotic Upper Keys-Mesophotic -0.065258181  0.00294638421
## 211    211 Upper Keys Mesophotic Upper Keys-Mesophotic -0.016955065 -0.02061242048
## 212    212 Upper Keys Mesophotic Upper Keys-Mesophotic -0.065777711 -0.00234690448
## 214    214 Upper Keys Mesophotic Upper Keys-Mesophotic  0.059578722  0.06163882428
## 216    216 Upper Keys Mesophotic Upper Keys-Mesophotic  0.048721852 -0.00442204082
## 217    217 Upper Keys Mesophotic Upper Keys-Mesophotic -0.064179159 -0.00003529347
## 218    218 Upper Keys    Shallow    Upper Keys-Shallow -0.071377029 -0.00438152639
## 219    219 Upper Keys    Shallow    Upper Keys-Shallow -0.068693656 -0.00181282943
## 220    220 Upper Keys    Shallow    Upper Keys-Shallow -0.074792005 -0.00403227742
## 222    222 Upper Keys    Shallow    Upper Keys-Shallow  0.024190252  0.05709267937
## 224    224 Upper Keys    Shallow    Upper Keys-Shallow -0.063284821  0.00195765540
## 225    225 Upper Keys    Shallow    Upper Keys-Shallow -0.067763657  0.00898885427
## 226    226 Upper Keys    Shallow    Upper Keys-Shallow -0.066022674 -0.00438777936
## 227    227 Upper Keys    Shallow    Upper Keys-Shallow -0.063271172 -0.00037414791
## 228    228 Upper Keys    Shallow    Upper Keys-Shallow -0.071794568 -0.00534499324
## 229    229 Upper Keys    Shallow    Upper Keys-Shallow  0.030634903  0.05235783277
## 230    230 Upper Keys    Shallow    Upper Keys-Shallow -0.077159133 -0.00732436888
## 231    231 Upper Keys    Shallow    Upper Keys-Shallow -0.072703242 -0.00703501858
## 232    232 Upper Keys    Shallow    Upper Keys-Shallow  0.022621692  0.04855444502
## 233    233 Upper Keys    Shallow    Upper Keys-Shallow  0.024225550  0.04568635764
## 234    234 Upper Keys    Shallow    Upper Keys-Shallow -0.063499916  0.00218060829
## 235    235 Upper Keys    Shallow    Upper Keys-Shallow -0.075537320  0.00067007824
## 236    236 Upper Keys    Shallow    Upper Keys-Shallow -0.064593148  0.00081026672
## 237    237 Upper Keys    Shallow    Upper Keys-Shallow -0.076257950 -0.00547105691
snpPCoA = merge(fkSnpPcoaValues, aggregate(cbind(mean.x=PCo1,mean.y=PCo2)~popsite, fkSnpPcoaValues, mean), by="popsite")

snpPCoA$depth=as.factor(snpPCoA$depth)
snpPCoA$depth = factor(snpPCoA$depth, levels(snpPCoA$depth)[c(2,1)])

# SNP PCoA biplot
fkSnpPcoaPlotA = ggplot(snpPCoA, aes(x = PCo1, y = PCo2, color = pop, fill = pop, shape = depth, linetype = depth)) +
  geom_hline(yintercept = 0, color = "gray90", size = 0.5) +
  geom_vline(xintercept = 0, color = "gray90", size = 0.5) +
  stat_ellipse(data = subset(snpPCoA, type = "t", geom = "polygon", alpha = 0.1)) + #ellipse
  scale_linetype_manual(values=c(1,2), breaks=c("Shallow","Mesophotic"), name = "Depth Zone")+
  geom_point(aes(x = PCo1, y = PCo2, shape = depth), size = 3, alpha = 0.3, show.legend = FALSE, guide=FALSE) + #individual's points indicated by circles
  scale_shape_manual(values = c(24,25), breaks=c("Shallow","Mesophotic"), name = "Depth Zone") +
  geom_point(aes(x = mean.x, y = mean.y, shape = depth), size = 5, color = "black") + #population centroids indicated by triangles
  scale_fill_paletteer_d("LaCroixColoR::PassionFruit", breaks=c("TER-South","TER-North","Lower Keys", "Upper Keys"), name= "Population", labels = c("DRTS", "DRTN", "LK", "UK"))+
  scale_color_paletteer_d("LaCroixColoR::PassionFruit", breaks=c("TER-South","TER-North","Lower Keys", "Upper Keys"), name = " Population", guide=FALSE) +
  xlab(paste ("PCo 1 (", fkSnpPcoaVar[1],"%)", sep = "")) + #Prints percent variation explained by first axis
  ylab(paste ("PCo 2 (", fkSnpPcoaVar[2],"%)", sep = "")) + #Prints percent variation explained by second axis
  guides(shape = guide_legend(order = 2), linetype = guide_legend(order = 3), fill = guide_legend(override.aes = list(shape = 22, size = 4, color = NA), order = 1))+
  theme_bw()

fkSnpPcoaPlot = fkSnpPcoaPlotA +
  theme(axis.title.x = element_text(color = "black", size = 10),
        axis.text.x = element_blank(),
        axis.ticks.x = element_blank(),
        axis.line.x = element_blank(),
        axis.title.y = element_text(color = "black", size = 10),
        axis.text.y = element_blank(),
        axis.ticks.y = element_blank(),
        axis.line.y = element_blank(),
        legend.position = "left",
        panel.border = element_rect(color = "black", size = 1.2),
        panel.background = element_rect(fill = "white"),
        plot.background = element_rect(fill = "white"),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())



fkSnpPcoaPlot

ggsave("../figures/fkSnpPcoaPlot.tiff", plot = fkSnpPcoaPlot, height = 5, width = 7, units = "in", dpi = 300)

AMOVA and Pairwise Fst

fkVcf = read.vcfR("fkMcavNoClonesRenamed.vcf.gz")
## Scanning file to determine attributes.
## File attributes:
##   meta lines: 12
##   header_line: 13
##   variant count: 9906
##   column count: 224
## 
Meta line 12 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 9906
##   Character matrix gt cols: 224
##   skip: 0
##   nrows: 9906
##   row_num: 0
## 
Processed variant 1000
Processed variant 2000
Processed variant 3000
Processed variant 4000
Processed variant 5000
Processed variant 6000
Processed variant 7000
Processed variant 8000
Processed variant 9000
Processed variant: 9906
## All variants processed
fkGenlightPopDepth = vcfR2genlight(fkVcf, n.cores = 2) # Converts the vcf file into a file format that poppr uses the "genlight" format
locNames(fkGenlightPopDepth) = paste(fkVcf@fix[,1],fkVcf@fix[,2],sep="_")
popData = read.csv("inds2popsNoClonesPopDepth.csv") # Reads in population data for each sample

strata(fkGenlightPopDepth) = data.frame(popData)
setPop(fkGenlightPopDepth) = ~popdepth
amova <- poppr.amova(fkGenlightPopDepth, ~popdepth) #Runs AMOVA
amova
## $call
## ade4::amova(samples = xtab, distances = xdist, structures = xstruct)
## 
## $results
##                                  Df    Sum Sq  Mean Sq
## Between popdepth                  7  21843.08 3120.440
## Between samples Within popdepth 207 257011.43 1241.601
## Within samples                  215 230160.00 1070.512
## Total                           429 509014.51 1186.514
## 
## $componentsofcovariance
##                                                  Sigma          %
## Variations  Between popdepth                  35.26104   2.959836
## Variations  Between samples Within popdepth   85.54474   7.180684
## Variations  Within samples                  1070.51163  89.859480
## Total variations                            1191.31740 100.000000
## 
## $statphi
##                             Phi
## Phi-samples-total    0.10140520
## Phi-samples-popdepth 0.07399703
## Phi-popdepth-total   0.02959836
set.seed(1999)
amovasignif <- randtest(amova, nrepet = 99) #Calculates significance levels of the AMOVA with 99 permutations
amovasignif
## class: krandtest lightkrandtest 
## Monte-Carlo tests
## Call: randtest.amova(xtest = amova, nrepet = 99)
## 
## Number of tests:   3 
## 
## Adjustment method for multiple comparisons:   none 
## Permutation number:   99 
##                          Test        Obs   Std.Obs   Alter Pvalue
## 1   Variations within samples 1070.51163 -8.817785    less   0.01
## 2  Variations between samples   85.54474  7.296027 greater   0.01
## 3 Variations between popdepth   35.26104 26.375609 greater   0.01
fkGenlightPopDepth$pop=as.factor(fkGenlightPopDepth$pop)
fkGenlightPopDepth$pop = factor(fkGenlightPopDepth$pop, levels(fkGenlightPopDepth$pop)[c(4,3,2,1,5,6,8,7)])

set.seed(694)
fk.fst <- stamppFst(fkGenlightPopDepth, nboots = 99, percent = 95, nclusters = 4) #99 permutations
fk.fst$Fsts
##                       TER-North-Mesophotic TER-North-Shallow TER-South-Mesophotic
## TER-North-Mesophotic                    NA                NA                   NA
## TER-North-Shallow              0.003785359                NA                   NA
## TER-South-Mesophotic           0.010043720       0.024102843                   NA
## TER-South-Shallow              0.029659330       0.012996675         0.0620714703
## Lower Keys-Shallow             0.020048949       0.009449199         0.0567990838
## Lower Keys-Mesophotic          0.013215768       0.033280930         0.0042096509
## Upper Keys-Mesophotic          0.007774893       0.020918576        -0.0007020888
## Upper Keys-Shallow             0.014999374       0.034087540         0.0030192813
##                       TER-South-Shallow Lower Keys-Shallow Lower Keys-Mesophotic
## TER-North-Mesophotic                 NA                 NA                    NA
## TER-North-Shallow                    NA                 NA                    NA
## TER-South-Mesophotic                 NA                 NA                    NA
## TER-South-Shallow                    NA                 NA                    NA
## Lower Keys-Shallow          0.003220882                 NA                    NA
## Lower Keys-Mesophotic       0.070866486         0.06483802                    NA
## Upper Keys-Mesophotic       0.062321097         0.05631169           0.007503063
## Upper Keys-Shallow          0.079599368         0.07217347           0.007040291
##                       Upper Keys-Mesophotic Upper Keys-Shallow
## TER-North-Mesophotic                     NA                 NA
## TER-North-Shallow                        NA                 NA
## TER-South-Mesophotic                     NA                 NA
## TER-South-Shallow                        NA                 NA
## Lower Keys-Shallow                       NA                 NA
## Lower Keys-Mesophotic                    NA                 NA
## Upper Keys-Mesophotic                    NA                 NA
## Upper Keys-Shallow               0.00359348                 NA
fk.fst$Pvalues
##                       TER-North-Mesophotic TER-North-Shallow TER-South-Mesophotic
## TER-North-Mesophotic                    NA                NA                   NA
## TER-North-Shallow                        0                NA                   NA
## TER-South-Mesophotic                     0                 0                   NA
## TER-South-Shallow                        0                 0                    0
## Lower Keys-Shallow                       0                 0                    0
## Lower Keys-Mesophotic                    0                 0                    0
## Upper Keys-Mesophotic                    0                 0                    1
## Upper Keys-Shallow                       0                 0                    0
##                       TER-South-Shallow Lower Keys-Shallow Lower Keys-Mesophotic
## TER-North-Mesophotic                 NA                 NA                    NA
## TER-North-Shallow                    NA                 NA                    NA
## TER-South-Mesophotic                 NA                 NA                    NA
## TER-South-Shallow                    NA                 NA                    NA
## Lower Keys-Shallow                    0                 NA                    NA
## Lower Keys-Mesophotic                 0                  0                    NA
## Upper Keys-Mesophotic                 0                  0                     0
## Upper Keys-Shallow                    0                  0                     0
##                       Upper Keys-Mesophotic Upper Keys-Shallow
## TER-North-Mesophotic                     NA                 NA
## TER-North-Shallow                        NA                 NA
## TER-South-Mesophotic                     NA                 NA
## TER-South-Shallow                        NA                 NA
## Lower Keys-Shallow                       NA                 NA
## Lower Keys-Mesophotic                    NA                 NA
## Upper Keys-Mesophotic                    NA                 NA
## Upper Keys-Shallow                        0                 NA
pop.order <- c("TER-South-Shallow", "TER-South-Mesophotic",  "TER-North-Shallow", "TER-North-Mesophotic", "Lower Keys-Shallow", "Lower Keys-Mesophotic", "Upper Keys-Shallow", "Upper Keys-Mesophotic")

# reads in fst matrix
snpFstMa <- as.matrix(fk.fst$Fsts)
upperTriangle(snpFstMa, byrow=TRUE) <- lowerTriangle(snpFstMa)
snpFstMa <- snpFstMa[,pop.order] %>%
  .[pop.order,]
snpFstMa[upper.tri(snpFstMa)] <- NA
snpFstMa <- as.data.frame(snpFstMa)

snpFstMa$Pop = factor(row.names(snpFstMa), levels = unique(pop.order))

snpQMa <- as.matrix(fk.fst$Pvalues)
upperTriangle(snpQMa, byrow=TRUE) <- lowerTriangle(snpQMa)
snpQMa <- snpQMa[,pop.order] %>%
  .[pop.order,]
snpQMa[upper.tri(snpQMa)] <- NA
snpQMa <- as.data.frame(snpQMa)
snpQMa$Pop = factor(row.names(snpQMa), levels = unique(pop.order))

snpFstMa$Pop = factor(row.names(snpFstMa), levels = unique(pop.order))
snpFst = melt(snpFstMa, id.vars = "Pop", value.name = "Fst", variable.name = "Pop2", na.rm = TRUE)
snpFst = snpFst[snpFst$Pop != snpFst$Pop2,]
snpFst$Fst = round(snpFst$Fst, 3)
snpFst = snpFst %>% mutate(Fst = replace(Fst, Fst < 0, 0))
head(snpFst)
##                     Pop              Pop2   Fst
## 2  TER-South-Mesophotic TER-South-Shallow 0.062
## 3     TER-North-Shallow TER-South-Shallow 0.013
## 4  TER-North-Mesophotic TER-South-Shallow 0.030
## 5    Lower Keys-Shallow TER-South-Shallow 0.003
## 6 Lower Keys-Mesophotic TER-South-Shallow 0.071
## 7    Upper Keys-Shallow TER-South-Shallow 0.080
snpQ = melt(snpQMa, id.vars = "Pop", value.name = "Pval", variable.name = "Pop2", na.rm = TRUE)
snpQ = snpQ[snpQ$Pop != snpQ$Pop2,]
snpQ$Qval = p.adjust(snpQ$Pval, method = "BH")
head(snpQ)
##                     Pop              Pop2 Pval Qval
## 2  TER-South-Mesophotic TER-South-Shallow    0    0
## 3     TER-North-Shallow TER-South-Shallow    0    0
## 4  TER-North-Mesophotic TER-South-Shallow    0    0
## 5    Lower Keys-Shallow TER-South-Shallow    0    0
## 6 Lower Keys-Mesophotic TER-South-Shallow    0    0
## 7    Upper Keys-Shallow TER-South-Shallow    0    0
snpHeatmapA = ggplot(data = snpFst, aes(Pop, Pop2, fill = Fst))+
  geom_tile(color = "white")+
  scale_fill_gradient2(low = "white", high = "red", midpoint = 0, limit = c(0, 0.1),
                       space = "Lab", name = expression(paste(italic("F")[ST])))+
  geom_text(data = snpFst, aes(Pop, Pop2, label = Fst), color = ifelse(snpQ$Qval <= 0.05,"black", "darkgrey"), size = ifelse(snpQ$Qval < 0.05, 6, 5)) +
  guides(fill=guide_colorbar(barwidth = 1, barheight = 12, title.position = "top", title.hjust = 0.5))+                     
  scale_y_discrete(position = "right", labels=c("DRTS-Shallow", "DRTS-Mesophotic", "DRTN-Shallow","DRTN-Mesophotic","LK-Shallow", "LK-Mesophotic", "UK-Shallow"))+
  scale_x_discrete(labels = str_wrap(c("DRTS-Mesophotic", "DRTN-Shallow","DRTN-Mesophotic","LK-Shallow", "LK-Mesophotic", "UK-Shallow", "UK-Mesophotic"), width = 6)) +
  #ggtitle("   SNP") +
  theme_minimal()

snpHeatmap = snpHeatmapA + theme(
  axis.text.x = element_text(vjust = 1, size = 16, hjust = 0.5, color = "black"),
  axis.text.y = element_text(size = 16, color = "black"),
  axis.title.x = element_blank(),
  axis.title.y = element_blank(),
  panel.grid.major = element_blank(),
  panel.border = element_blank(),
  panel.background = element_blank(),
  axis.ticks = element_blank(),
  legend.position = "right",
  legend.direction = "vertical",
  legend.title = element_text(size = 16),
  legend.text = element_text(size = 14),
  plot.title = element_text(size = 16)
)

snpHeatmap

ggsave("../figures/snpHeatMap.tiff", plot = snpHeatmap, width = 34, height = 15, units = "cm", dpi = 300)

ADMIXTURE Plot

# df1 <- read.csv("fkMcavNoClones_k4.csv")
# admixedSamples=filter(df1, cluster1 < 0.75, cluster2 < 0.75, cluster3 < 0.75, cluster4 < 0.75)
# count(admixedSamples$pop)

df <- read.csv("fkMcavNoClones_k4.csv")
df$sample <- factor(df$sample, levels= df$sample[order(-df$cluster4, df$cluster2)])
mdat = melt(df, id.vars=c("sample", "pop"), variable.name="Ancestry", value.name="Fraction")
mdat$pop=as.factor(mdat$pop)
mdat$pop = factor(mdat$pop, levels(mdat$pop)[c(6,5,4,3,2,1,8,7)])
levels(mdat$pop) = c("DRTS-Shallow", "DRTS-Mesophotic", "DRTN-Shallow", "DRTN-Mesophotic", "LK-Shallow", "LK-Mesophotic", "UK-Shallow", "UK-Mesophotic")

p = ggplot(mdat, aes(x=sample, y=Fraction, fill=Ancestry)) +
  geom_bar(stat="identity", position="stack") +
  facet_grid(.~pop, drop=TRUE, space="free", scales="free")
#col2 = c("turquoise", "blue", "green", "purple")
#names(col2) = levels(mdat$Ancestry)
p2 = ggplot(mdat, aes(x=sample, y=Fraction, fill=Ancestry, order=sample)) +
  geom_bar(stat="identity", position="fill", width=1, colour="grey25") +
  facet_grid(.~pop, scales = "free", switch = "x", space = "free") +
  labs(x = "Population", y = "Ancestry") +
  #ggtitle("K4 NGSAdmixture Plot") +
  theme(plot.title = element_text(hjust = 0.5),
  panel.grid=element_blank(),
  panel.background=element_rect(fill=NA, colour="grey25"),
  panel.spacing.x=grid:::unit(0, "lines"),
  panel.border = element_rect(fill=NA,color="black", size=2, linetype="solid"),
  #axis.text.x=element_text(size=12, angle=90)
  axis.text.x = element_blank(),
  axis.ticks.x=element_blank(),
  strip.background=element_blank(),
  strip.text=element_text(size=12, angle=90),
  legend.key=element_blank(),
  legend.position = "none",
  legend.title = element_blank()) +
  scale_x_discrete(expand=c(0, 0)) +
  scale_y_continuous(expand=c(0, 0)) +
  scale_fill_manual(values = brewer.pal(name = "YlGnBu", n = 4), name = "Cluster") +
  guides(fill=guide_legend(override.aes=list(colour=NULL)))
p2

ggsave("../figures/admixturePlot.tiff", plot = p2, width = 30, height = 15, units = "cm", dpi = 300)

Zoox and Depth

zooxHostProportions=read.csv("zooxMcavRatio.csv", header=TRUE)
skewness(zooxHostProportions$zooxReadRatio, na.rm = TRUE)
zooxHostProportions$zooxReadRatio <- log10(zooxHostProportions$zooxReadRatio)
skewness(zooxHostProportions$zooxReadRatio, na.rm = TRUE)

zooxDepthPlot=ggplot(zooxHostProportions, aes(x=depth, y=zooxReadRatio)) +
  geom_point()+
  geom_smooth(method = "lm")

zooxDepthPlot

leveneTest(zooxReadRatio ~ site*depthZone, data = zooxHostProportions)
res.aov3 <- aov(zooxReadRatio ~ site * depthZone, data = zooxHostProportions)
shapiro.test(zooxHostProportions$zooxReadRatio)
residualplot=plot(res.aov3, 2)
zooxAnova <- aov(zooxReadRatio ~ site * depthZone, data = zooxHostProportions)
Anova(zooxAnova, type = "III")


lsmeans = lsmeans::lsmeans ### Uses the lsmeans function
                           ###  from the lsmeans package,
                           ###  not from the lmerTest package

leastsquare = lsmeans(zooxAnova,
                      pairwise ~ site:depthZone,
                      adjust="tukey")


zooxBoxPlot=ggplot(zooxHostProportions, aes(x=site, y=zooxReadRatio, fill=depthZone)) +
  geom_boxplot()

zooxBoxPlot


#Zoox Plot

dfZoox = read.csv("zooxCommunity.csv")

dfZoox$Population = factor(dfZoox$Population, levels = levels(dfZoox$Population)[c(6,5,4,3,2,1,8,7)])

dfZoox = dfZoox[order(dfZoox$Population),]
dfZoox$Order = c(1:nrow(dfZoox))

zDat = melt(dfZoox, id.vars = c("Sample", "Population", "Order"), variable.name = "Symbiont", value.name = "Fraction")
colPalZoox = brewer.pal(4, "BrBG")
names(colPalZoox) = levels(zDat$Symbiont)

zooxPlotA = ggplot(data = zDat, aes(x = Order, y = Fraction, fill = Symbiont, order = Order)) +
  geom_bar(stat = "identity", position = "stack", colour = "grey25", width = 1) +
  xlab("Population") +
  scale_x_discrete(expand = c(0, 0)) +
  scale_y_continuous(expand = c(0, 0), labels = function(x) paste0(x*100, "%")) +
  scale_fill_manual(values = colPalZoox, name = "Symbiodiniaceae genus") +
  coord_cartesian(ylim = c(-.01,1.01)) +
  facet_grid(.~fct_inorder(Population), drop=TRUE, scales = "free", switch = "x", space = "free") +
  theme_bw()

zooxPlot = zooxPlotA + theme(plot.title = element_text(hjust = 0.5),
  panel.grid=element_blank(),
  panel.background=element_rect(fill=NA, colour="grey25"),
  panel.spacing.x=grid:::unit(0, "lines"),
  panel.border = element_rect(fill=NA,color="black", size=2, linetype="solid"),
  #axis.text.x=element_text(size=12, angle=90)
  axis.text.x = element_blank(),
  axis.ticks.x=element_blank(),
  strip.background=element_blank(),
  strip.text=element_text(size=12, angle=90),
  legend.key=element_blank(),
  legend.position = "right",
  legend.title = element_blank(),
  legend.text = element_text(face = "italic"))
zooxPlot

ggsave("../figures/zooxPlot.tiff", plot = zooxPlot, width = 30, height = 15, units = "cm", dpi = 300)
# Isolation by distance
ReplaceLowerOrUpperTriangle = function(m, triangle.to.replace) {
  if (nrow(m) != ncol(m))
    stop("Supplied matrix must be square.")
  if (tolower(triangle.to.replace) == "lower")
    tri = lower.tri(m)
  else if (tolower(triangle.to.replace) == "upper")
    tri = upper.tri(m)
  else
    stop("triangle.to.replace must be set to 'lower' or 'upper'.")
  m[tri] = t(m)[tri]
  return(m)
}
  # If triangle.to.replace="lower", replaces the lower triangle of a square matrix with its upper triangle.
  # If triangle.to.replace="upper", replaces the upper triangle of a square matrix with its lower triangle.

GeoDistanceInMetresMatrix = function(df.geopoints) {
  # Returns a matrix (M) of distances between geographic points. M[i,j] = M[j,i] = Distance between (df.geopoints$lat[i], df.geopoints$lon[i]) and (df.geopoints$lat[j], df.geopoints$lon[j]). The row and column names are given by df.geopoints$name.
  
  GeoDistanceInMetres = function(g1, g2) {
    # Returns a vector of distances. (But if g1$index > g2$index, returns zero.) The 1st value in the returned vector is the distance between g1[[1]] and g2[[1]]. The 2nd value in the returned vector is the distance between g1[[2]] and g2[[2]]. Etc. Each g1[[x]] or g2[[x]] must be a list with named elements "index", "lat" and "lon". E.g. g1 = list(list("index"=1, "lat"=12.1, "lon"=10.1), list("index"=3, "lat"=12.1, "lon"=13.2))
    
    DistM = function(g1, g2) {
      require("Imap")
      return(ifelse(
        g1$index > g2$index,
        0,
        gdist(lat.1 = g1$lat, lon.1 = g1$lon, lat.2 = g2$lat, lon.2 = g2$lon, units = "m")))
    }
    return(mapply(DistM, g1, g2))
  }
  
  n.geopoints = nrow(df.geopoints)
  
  # The index column is used to ensure we only do calculations for the upper triangle of points
  df.geopoints$index = 1:n.geopoints
  
  # Create a list of lists
  list.geopoints = by(df.geopoints[, c("index", "lat", "lon")], 1:n.geopoints, function(x) {
    return(list(x))
  })
  
  # Get a matrix of distances (in metres)
  mat.distances = ReplaceLowerOrUpperTriangle(outer(list.geopoints, list.geopoints, GeoDistanceInMetres), "lower")
  
  # Set the row and column names
  rownames(mat.distances) = df.geopoints$name
  colnames(mat.distances) = df.geopoints$name
  return(mat.distances)}

snpNeiDist = as.dist(stamppNeisD(fkGenlightPopDepth, pop = TRUE), diag = F)
coords = read.csv("fkXYcoords.csv", header=TRUE) # tab-separated file for all pops
dGeo = as.dist(GeoDistanceInMetresMatrix(coords)/1000, diag = T)

# Test IBD
set.seed(694)
snpIBD = mantel.randtest(dGeo,snpNeiDist)
snpIBD
## Monte-Carlo test
## Call: mantel.randtest(m1 = dGeo, m2 = snpNeiDist)
## 
## Observation: -0.02800992 
## 
## Based on 999 replicates
## Simulated p-value: 0.496 
## Alternative hypothesis: greater 
## 
##      Std.Obs  Expectation     Variance 
## -0.181032369  0.006993677  0.037386334
snpNei =  melt(as.matrix(snpNeiDist), varnames = c("row", "col"), value.name = "nei")
snpNei = snpNei[snpNei$row != snpNei$col,]

geo = melt(as.matrix(dGeo), varnames = c("row", "col"), value.name = "geo")
geo = geo[geo$row != geo$col,]

snpMantelDF = data.frame(cbind(snpNei$nei, geo$geo))
colnames(snpMantelDF) = c("nei", "geo")

snpMantelA = ggplot(data = snpMantelDF, aes(x = geo, y = nei)) +
  scale_fill_gradientn(colors = paletteer_d("wesanderson::Zissou1")) +
  stat_density_2d(aes(fill = stat(density)), n = 300, contour = FALSE, geom = "raster") +
  geom_smooth(method = lm, col = "black", fill = "gray40", fullrange = TRUE) +
  geom_point(shape = 21, fill = "gray40") +
  scale_x_continuous(limits = c(0,1000), expand = c(0,0)) +
  scale_y_continuous(limits = c(0,0.15), breaks = seq(0,0.15, by = 0.05), expand = c(0,0)) +
  annotate("label", x = 775, y = 0.14325, 
           label = paste("r = ", round(snpIBD$obs, 3), "; p = ", snpIBD$pvalue), 
           size = 4, alpha = 0.6) +             
  labs(x = "Geographic distance (km)", y = expression(paste("Nei's genetic distance (",italic("D"),")"))) +
  ggtitle("SNP") +
  theme_bw()

snpMantel = snpMantelA + theme(
  axis.title.x = element_blank(),
  axis.text.x = element_text(size = 12, color = "black"),
  axis.ticks.x = element_line(color = "black"),
  axis.line.x = element_blank(),
  axis.title.y = element_text(color = "white"),
  axis.text.y = element_text(size = 12, color = "black"),
  axis.ticks.y = element_line(color = "black"),
  axis.line.y = element_blank(),
  panel.border = element_rect(size = 1.2, color = "black"),
  plot.margin = margin(0.2,0.5,0.1,0.1, unit = "cm"),
  legend.position = "none")

snpMantel
## `geom_smooth()` using formula 'y ~ x'

source('plot_R.r')

dat = read.table("fkMcav.baye_fst.txt",header=T)
head(dat)
##       prob  log10.PO.     qval     alpha      fst
## 1 0.117624   -0.87516 0.675734 -0.100360 0.027392
## 2 0.077215   -1.07740 0.835710 -0.036717 0.028434
## 3 0.071014   -1.11670 0.853910 -0.017603 0.028814
## 4 1.000000 1000.00000 0.000000  1.625500 0.131590
## 5 0.076215   -1.08350 0.839110 -0.025847 0.028704
## 6 0.082216   -1.04780 0.819380  0.033438 0.030727
table(dat[,"qval"]<0.1)
## 
## FALSE  TRUE 
##  9575   331
outs=which(dat[,"qval"]<0.1)
plot_bayescan("fkMcav.baye_fst.txt",FDR=0.1,add_text=F,size=0.5,highlight=outs)

## $outliers
##   [1]    4   63   79   90   91  153  164  174  191  194  195  257  266  355  356  368
##  [17]  370  372  386  498  547  571  619  632  637  672  673  703  759  776  788  793
##  [33]  799  813  815  868  878  885  904  955  994 1003 1004 1073 1095 1138 1167 1187
##  [49] 1191 1247 1290 1315 1320 1344 1420 1421 1511 1541 1580 1581 1602 1603 1621 1641
##  [65] 1646 1658 1716 1733 1822 1868 1918 1925 2004 2014 2025 2026 2027 2036 2042 2048
##  [81] 2066 2089 2091 2092 2174 2245 2257 2269 2304 2307 2311 2349 2353 2379 2411 2436
##  [97] 2438 2439 2470 2479 2540 2576 2590 2594 2595 2621 2639 2657 2716 2871 2891 2905
## [113] 2912 2916 2989 3000 3002 3009 3060 3064 3097 3135 3136 3160 3212 3243 3244 3274
## [129] 3396 3605 3687 3697 3702 3731 3732 3876 3903 4032 4033 4081 4184 4205 4255 4280
## [145] 4320 4323 4369 4385 4402 4404 4489 4495 4508 4523 4530 4538 4610 4612 4623 4641
## [161] 4643 4654 4678 4684 4703 4717 4734 4743 4781 4817 4824 4885 4886 4901 4961 5025
## [177] 5040 5114 5124 5166 5199 5202 5203 5244 5264 5286 5287 5326 5385 5386 5393 5401
## [193] 5424 5441 5469 5476 5509 5512 5546 5577 5605 5611 5692 5700 5705 5743 5760 5765
## [209] 5769 5775 5780 5801 5842 5971 6040 6042 6068 6070 6095 6106 6132 6138 6144 6170
## [225] 6191 6288 6310 6326 6444 6465 6525 6551 6573 6612 6649 6666 6671 6679 6713 6812
## [241] 6886 6893 6935 7043 7083 7088 7111 7146 7191 7235 7276 7403 7411 7531 7577 7596
## [257] 7607 7650 7661 7681 7689 7749 7787 7869 7906 7922 8033 8049 8106 8108 8114 8116
## [273] 8117 8147 8184 8227 8261 8262 8309 8390 8490 8496 8510 8511 8527 8543 8552 8611
## [289] 8731 8732 8739 8855 8858 8872 8932 8980 9017 9018 9074 9078 9104 9132 9160 9210
## [305] 9224 9258 9364 9367 9389 9437 9456 9457 9458 9465 9504 9519 9523 9533 9557 9601
## [321] 9644 9646 9648 9722 9723 9725 9745 9806 9807 9810 9893
## 
## $nb_outliers
## [1] 331
#Minor Allele Frequencies of Outliers Across Populations
outAlleleFreq=read.csv("outlierAlleleFreqs.csv")
outAlleleFreqPlot <- ggplot(outAlleleFreq, aes(x=PopDepth, y=MIF)) + 
  geom_boxplot()+
  theme_bw()
outAlleleFreqPlot

outAlleleFreq.lm = lm(MIF ~ AvgDepth, data=outAlleleFreq)
summary(outAlleleFreq.lm)$r.squared 
## [1] 0.007696518
ggplot(outAlleleFreq, aes(x=AvgDepth, y=MIF)) + geom_point()+ geom_smooth(method=lm)
## `geom_smooth()` using formula 'y ~ x'

SNPs potentially under selection

genes = read.table("mcav_gene_regions.tab")
names(genes) = c("chromo","start","end","gene")

# expand gene regions ± 2000 bp
genes$start = genes$start -2000
genes$end = genes$end +2000

gnames = read.table("mcav_cog.txt", sep = "\t")
names(gnames) = c("gene", "cog", "protein")

genes = full_join(genes, gnames, by = "gene")
genes$protein=as.character(genes$protein)
genes$protein[is.na(genes$protein)]="unknown"

#how many annotated genes do we have?
nrow(genes[genes$protein!="unknown",])
## [1] 9912
head(genes)
##      chromo  start    end            gene  cog
## 1 Sc0000101  17738  46551 Mcavernosa04235 <NA>
## 2 Sc0000101 113438 122548 Mcavernosa04241 <NA>
## 3 Sc0000101 105283 117140 Mcavernosa04239 <NA>
## 4 Sc0000101 182029 186424 Mcavernosa04243    F
## 5 Sc0000101 118230 122978 Mcavernosa04242 <NA>
## 6 Sc0000101 104867 111016 Mcavernosa04238    L
##                                                    protein
## 1                                                  unknown
## 2                                                  unknown
## 3                                                  unknown
## 4                                         (dCMP) deaminase
## 5                                                  unknown
## 6 Inherit from meNOG: multicellular organismal development
snpLoci = read.table("fkMcavNoClones.mafs.gz", header = TRUE)
snpLoci$locus = c(1:nrow(snpLoci))

outsByGene = snpLoci %>% dplyr::select(locus, chromo, position) %>% 
  filter(locus %in% outs) %>%
  full_join(., genes, by = "chromo") %>% 
  filter(position>start, position<end)

outsByGene
##     locus      chromo position   start     end            gene  cog
## 1       4   Sc0000000   133071  132438  155504 Mcavernosa06199 <NA>
## 2      63   Sc0000001   841002  833885  847804 Mcavernosa06411 <NA>
## 3      90   Sc0000001  1690037 1687505 1692512 Mcavernosa06481 <NA>
## 4      91   Sc0000001  1690055 1687505 1692512 Mcavernosa06481 <NA>
## 5     153   Sc0000003   380756  368792  393150 Mcavernosa06686 <NA>
## 6     164   Sc0000003   576184  567380  579867 Mcavernosa06707 <NA>
## 7     174   Sc0000003   785938  784603  799509 Mcavernosa06724 <NA>
## 8     191   Sc0000003  1236302 1231990 1241385 Mcavernosa06771 <NA>
## 9     266   Sc0000005   415610  413324  422027 Mcavernosa06992 <NA>
## 10    355   Sc0000007   832690  823671  835359 Mcavernosa00064    B
## 11    356   Sc0000007   880296  878147  888205 Mcavernosa00072    K
## 12    368   Sc0000007  1337188 1330506 1340868 Mcavernosa00118 T, U
## 13    370   Sc0000008    50620   45346   51860 Mcavernosa00133 <NA>
## 14    372   Sc0000008    58676   56915   71673 Mcavernosa00135    O
## 15    372   Sc0000008    58676   55911   60813 Mcavernosa00134    F
## 16    386   Sc0000008   503055  492721  503102 Mcavernosa00187    O
## 17    386   Sc0000008   503055  502715  507847 Mcavernosa00189 <NA>
## 18    386   Sc0000008   503055  501330  506280 Mcavernosa00188 <NA>
## 19    547   Sc0000012    48483   47025   51570 Mcavernosa00675 <NA>
## 20    632   Sc0000015   159724  145156  161161 Mcavernosa01022    O
## 21    637   Sc0000015   403215  394822  404933 Mcavernosa01046 <NA>
## 22    759   Sc0000018   792663  771401  794949 Mcavernosa01502 <NA>
## 23    776   Sc0000019   161993  160590  169407 Mcavernosa01711    S
## 24    788   Sc0000019   442489  438004  446586 Mcavernosa01737    I
## 25    793   Sc0000019   706060  700863  720685 Mcavernosa01750    F
## 26    885   Sc0000022   239151  237450  248306 Mcavernosa01985    T
## 27    904   Sc0000022   699099  696305  710712 Mcavernosa02040 <NA>
## 28    955   Sc0000024   279084  277990  287503 Mcavernosa03257 <NA>
## 29    994   Sc0000025   275188  273853  278737 Mcavernosa03361    K
## 30   1003   Sc0000025   482056  472108  487567 Mcavernosa03375    O
## 31   1003   Sc0000025   482056  480195  487577 Mcavernosa03377    O
## 32   1004   Sc0000025   482065  472108  487567 Mcavernosa03375    O
## 33   1004   Sc0000025   482065  480195  487577 Mcavernosa03377    O
## 34   1073   Sc0000028   801272  800600  817320 Mcavernosa03681    K
## 35   1191   Sc0000032   605694  602960  624431 Mcavernosa04030 <NA>
## 36   1247   Sc0000034   405029  399978  407510 Mcavernosa04174 <NA>
## 37   1290   Sc0000035   241187  216273  248825 Mcavernosa07247    T
## 38   1315   Sc0000036  1013464 1009475 1020750 Mcavernosa07364 <NA>
## 39   1344   Sc0000038   330324  327965  335330 Mcavernosa07636 <NA>
## 40   1420   Sc0000041   414564  387188  417847 Mcavernosa07881 <NA>
## 41   1420   Sc0000041   414564  411811  421571 Mcavernosa07882 <NA>
## 42   1421   Sc0000041   414834  387188  417847 Mcavernosa07881 <NA>
## 43   1421   Sc0000041   414834  411811  421571 Mcavernosa07882 <NA>
## 44   1511   Sc0000044   655362  655026  663660 Mcavernosa08189 <NA>
## 45   1580   Sc0000048    68340   59945   79936 Mcavernosa24515 <NA>
## 46   1581   Sc0000048    71757   59945   79936 Mcavernosa24515 <NA>
## 47   1602   Sc0000048   780568  776755  781852 Mcavernosa24579    K
## 48   1621   Sc0000049   677814  676938  691658 Mcavernosa24636    O
## 49   1641   Sc0000050   345719  339508  345869 Mcavernosa24682    U
## 50   1641   Sc0000050   345719  343656  351153 Mcavernosa24683    S
## 51   1646   Sc0000050   426445  422229  428942 Mcavernosa24692 <NA>
## 52   1733   Sc0000053   657280  651154  661769 Mcavernosa24928    K
## 53   1868   Sc0000059   742919  739262  755469 Mcavernosa16434 <NA>
## 54   1918   Sc0000062    38808   26976   48049 Mcavernosa16630    O
## 55   1925   Sc0000062   295853  281605  298921 Mcavernosa16657    T
## 56   2025   Sc0000066   650888  644107  676724 Mcavernosa16979    S
## 57   2026   Sc0000066   652197  644107  676724 Mcavernosa16979    S
## 58   2027   Sc0000066   654108  644107  676724 Mcavernosa16979    S
## 59   2042   Sc0000067   284567  278061  285961 Mcavernosa17017    P
## 60   2042   Sc0000067   284567  282441  289151 Mcavernosa17018    P
## 61   2089   Sc0000069   241430  230216  242726 Mcavernosa17168    S
## 62   2091   Sc0000069   259168  255860  261193 Mcavernosa17170 <NA>
## 63   2091   Sc0000069   259168  250294  259857 Mcavernosa17169    K
## 64   2092   Sc0000069   259171  255860  261193 Mcavernosa17170 <NA>
## 65   2092   Sc0000069   259171  250294  259857 Mcavernosa17169    K
## 66   2245   Sc0000075   616525  607578  618954 Mcavernosa02407    C
## 67   2269   Sc0000077   132592  126071  206963 Mcavernosa02504    S
## 68   2304   Sc0000078   538250  533613  551888 Mcavernosa02598    O
## 69   2307   Sc0000078   614585  613259  619758 Mcavernosa02606    L
## 70   2311   Sc0000079   250813  238726  255446 Mcavernosa02643    T
## 71   2311   Sc0000079   250813  248660  262153 Mcavernosa02644    T
## 72   2349   Sc0000080   361792  358370  363365 Mcavernosa02782 <NA>
## 73   2349   Sc0000080   361792  360415  371754 Mcavernosa02783    T
## 74   2353   Sc0000080   488331  487227  499585 Mcavernosa02799    S
## 75   2379   Sc0000082    92075   81308   92957 Mcavernosa02895    T
## 76   2379   Sc0000082    92075   90633  109672 Mcavernosa02896    O
## 77   2411   Sc0000084    35373   33192   72247 Mcavernosa03031    Q
## 78   2470   Sc0000088   271450  264057  273126 Mcavernosa30892    L
## 79   2479   Sc0000088   569845  564839  570315 Mcavernosa30922    S
## 80   2621   Sc0000096   477994  472669  480386 Mcavernosa31383 <NA>
## 81   2639   Sc0000097   272642  263264  286159 Mcavernosa31430 <NA>
## 82   2657   Sc0000098    71150   66657   78361 Mcavernosa31460 <NA>
## 83   2716   Sc0000100   537922  530213  540384 Mcavernosa31618 <NA>
## 84   2871   Sc0000110   465061  459333  473275 Mcavernosa04749    L
## 85   2905   Sc0000114    15141    3350   16689 Mcavernosa04908 <NA>
## 86   2912   Sc0000114   176790  175614  186976 Mcavernosa04926 <NA>
## 87   2916   Sc0000114   361540  348717  361889 Mcavernosa04940 <NA>
## 88   2916   Sc0000114   361540  360545  381336 Mcavernosa04941 <NA>
## 89   2989   Sc0000119   156354  152125  158165 Mcavernosa05289 <NA>
## 90   3000   Sc0000120    73156   72837   97288 Mcavernosa05333 <NA>
## 91   3000   Sc0000120    73156   71433   76045 Mcavernosa05332 <NA>
## 92   3009   Sc0000120   193690  181368  195746 Mcavernosa05341 <NA>
## 93   3064   Sc0000123   556926  543310  559927 Mcavernosa05548 <NA>
## 94   3097   Sc0000125    30700   30571   35101 Mcavernosa05607 <NA>
## 95   3135   Sc0000127    94790   88800  100135 Mcavernosa05715 <NA>
## 96   3160   Sc0000128   542816  529836  561530 Mcavernosa05780 <NA>
## 97   3212   Sc0000131   100946   93463  119509 Mcavernosa05895 <NA>
## 98   3274   Sc0000135   151402  148778  153866 Mcavernosa06086 <NA>
## 99   3396   Sc0000143   233814  224785  238979 Mcavernosa12556    T
## 100  3605   Sc0000156   233175  232263  242297 Mcavernosa13321    Z
## 101  3687   Sc0000162   271434  263202  272051 Mcavernosa13626 T, U
## 102  3697   Sc0000163   156786  154135  178495 Mcavernosa13675    F
## 103  3702   Sc0000163   476311  449149  476793 Mcavernosa13698    T
## 104  3731   Sc0000165    41199   36908   45903 Mcavernosa13845    I
## 105  3732   Sc0000165   109520  101511  128726 Mcavernosa13852    L
## 106  3876   Sc0000173   294276  269015  303285 Mcavernosa14217 <NA>
## 107  3903   Sc0000175    37460   36159   53720 Mcavernosa27805 <NA>
## 108  3903   Sc0000175    37460   34993   45023 Mcavernosa27804 <NA>
## 109  4032   Sc0000184    34744   30950   36777 Mcavernosa28265 <NA>
## 110  4033   Sc0000184    34745   30950   36777 Mcavernosa28265 <NA>
## 111  4081   Sc0000187   101619  100272  105105 Mcavernosa28458 <NA>
## 112  4081   Sc0000187   101619   92253  102976 Mcavernosa28457 <NA>
## 113  4280   Sc0000200   295534  286186  309693 Mcavernosa08605 <NA>
## 114  4323   Sc0000203   157445  155494  167885 Mcavernosa08740    K
## 115  4402   Sc0000209   350281  347785  365259 Mcavernosa09014    A
## 116  4404   Sc0000210   164055  158822  165206 Mcavernosa09023    O
## 117  4489   Sc0000216   311217  285965  314077 Mcavernosa14323    T
## 118  4495   Sc0000217    46907   46190   51038 Mcavernosa14336 <NA>
## 119  4508   Sc0000218   382711  373531  387331 Mcavernosa14417 <NA>
## 120  4530   Sc0000221    39889   39882   46317 Mcavernosa14539 <NA>
## 121  4538   Sc0000221   445181  420545  445853 Mcavernosa14579 T, W
## 122  4538   Sc0000221   445181  423988  445704 Mcavernosa14580 <NA>
## 123  4538   Sc0000221   445181  443025  456073 Mcavernosa14581    S
## 124  4610   Sc0000227   373213  368055  374347 Mcavernosa14835 <NA>
## 125  4612   Sc0000227   405468  401584  406889 Mcavernosa14838    Q
## 126  4623   Sc0000228   430154  428072  434242 Mcavernosa14875 <NA>
## 127  4654   Sc0000230   214219  210931  218813 Mcavernosa14928    S
## 128  4684   Sc0000232   390834  379259  409857 Mcavernosa15121    K
## 129  4703   Sc0000233   271811  265838  278226 Mcavernosa15141 <NA>
## 130  4781   Sc0000237   411631  404642  414672 Mcavernosa15300 <NA>
## 131  4885   Sc0000246   158533  150339  165139 Mcavernosa11524    O
## 132  4886   Sc0000246   160029  150339  165139 Mcavernosa11524    O
## 133  5025   Sc0000257   342541  337845  344749 Mcavernosa11977 <NA>
## 134  5040   Sc0000260   319736  319323  346737 Mcavernosa12107 <NA>
## 135  5114   Sc0000266   126940   95662  132659 Mcavernosa31702 <NA>
## 136  5124   Sc0000266   386573  379862  387378 Mcavernosa31728 <NA>
## 137  5124   Sc0000266   386573  385359  395709 Mcavernosa31731 <NA>
## 138  5203   Sc0000274   356889  326224  356983 Mcavernosa31974    T
## 139  5244   Sc0000280   366163  364767  372154 Mcavernosa32117 E, I
## 140  5264   Sc0000284   186309  183546  206825 Mcavernosa32213    S
## 141  5287   Sc0000287   272412  265916  289527 Mcavernosa32317    P
## 142  5385   Sc0000297   172951  168869  196246 Mcavernosa18360 <NA>
## 143  5386   Sc0000297   172959  168869  196246 Mcavernosa18360 <NA>
## 144  5393   Sc0000299    46600   38716   47500 Mcavernosa18484 <NA>
## 145  5401   Sc0000300   196983  196221  202231 Mcavernosa18527 <NA>
## 146  5441   Sc0000303    73881   66298   83229 Mcavernosa18619 <NA>
## 147  5476   Sc0000306   296046  276974  304185 Mcavernosa18753 <NA>
## 148  5509   Sc0000311   306679  301233  311954 Mcavernosa18887 <NA>
## 149  5577   Sc0000319   319167  310661  330433 Mcavernosa19142 <NA>
## 150  5605   Sc0000325   300798  290447  303700 Mcavernosa19307 <NA>
## 151  5605   Sc0000325   300798  300423  310063 Mcavernosa19308 <NA>
## 152  5611   Sc0000327    38091   23293   42444 Mcavernosa19334 <NA>
## 153  5700   Sc0000336   103052  101634  109113 Mcavernosa19615 <NA>
## 154  5705   Sc0000336   232381  225498  234939 Mcavernosa19631 <NA>
## 155  5760   Sc0000345   152147  147574  158683 Mcavernosa19881 A, J
## 156  5769   Sc0000346    94998   93359   99925 Mcavernosa19908    G
## 157  5775   Sc0000346   252012  250464  258089 Mcavernosa19923    S
## 158  5780   Sc0000347   151002  149194  159410 Mcavernosa19943 <NA>
## 159  5801   Sc0000350   197049  196914  207639 Mcavernosa20016    A
## 160  5842   Sc0000354   127506  126707  132765 Mcavernosa21924 B, K
## 161  5842   Sc0000354   127506  121023  128066 Mcavernosa21923    K
## 162  5971   Sc0000370   209590  206117  245168 Mcavernosa22382    Z
## 163  6040   Sc0000382   126036  124404  130113 Mcavernosa22726    S
## 164  6068   Sc0000386   218550  205378  219577 Mcavernosa15422    S
## 165  6068   Sc0000386   218550  216541  229696 Mcavernosa15423    O
## 166  6070   Sc0000386   218553  205378  219577 Mcavernosa15422    S
## 167  6070   Sc0000386   218553  216541  229696 Mcavernosa15423    O
## 168  6095   Sc0000389   100840   85399  108688 Mcavernosa15490 T, Z
## 169  6106   Sc0000390    96448   92122  109465 Mcavernosa15521    S
## 170  6132   Sc0000392   276515  262325  278763 Mcavernosa15635    Z
## 171  6138   Sc0000395    53353   48635   58418 Mcavernosa15712    S
## 172  6144   Sc0000395   228985  227146  239730 Mcavernosa15724    S
## 173  6170   Sc0000398   209284  208874  217574 Mcavernosa15811    A
## 174  6170   Sc0000398   209284  203599  212365 Mcavernosa15810    T
## 175  6191   Sc0000401    73136   69814   86271 Mcavernosa15895    T
## 176  6310   Sc0000421    19067   12129   20988 Mcavernosa10317 <NA>
## 177  6310   Sc0000421    19067   14826   29022 Mcavernosa10318 <NA>
## 178  6444   Sc0000440   119582  114625  144945 Mcavernosa10812 <NA>
## 179  6465   Sc0000443    56694   52892   66115 Mcavernosa10901 <NA>
## 180  6525   Sc0000454   173146  166175  184672 Mcavernosa11173 <NA>
## 181  6573   Sc0000461    78244   76666   84641 Mcavernosa09358 <NA>
## 182  6573   Sc0000461    78244   65552   79875 Mcavernosa09357 <NA>
## 183  6612   Sc0000465   102579   87010  114820 Mcavernosa09451 <NA>
## 184  6649   Sc0000473   194888  190194  197753 Mcavernosa09624 <NA>
## 185  6671   Sc0000478    84729   81991   86752 Mcavernosa09719    F
## 186  6713   Sc0000487   228045  223710  231967 Mcavernosa09976 <NA>
## 187  6935   Sc0000533    16564   14823   47062 Mcavernosa21637 <NA>
## 188  7088   Sc0000564    41161   40367   46799 Mcavernosa26807 P, T
## 189  7111   Sc0000568    75761   73400   77942 Mcavernosa26898 <NA>
## 190  7146   Sc0000576   103072  100970  107264 Mcavernosa27004    L
## 191  7191   Sc0000586    61007   54497   64743 Mcavernosa20087    F
## 192  7235   Sc0000596   132906  131076  168692 Mcavernosa20343    T
## 193  7596   Sc0000666   125771  123575  128137 Mcavernosa17889 <NA>
## 194  7650   Sc0000680   151817  149039  155842 Mcavernosa18111    S
## 195  7661   Sc0000682   137909  127400  138441 Mcavernosa18143    S
## 196  7681   Sc0000686   120700  116433  126374 Mcavernosa22820 <NA>
## 197  7689   Sc0000691    93534   87294   99827 Mcavernosa22890    E
## 198  7749   Sc0000713   106608  105346  111221 Mcavernosa23168    G
## 199  7787   Sc0000730    61782   58333   64367 Mcavernosa23327 <NA>
## 200  7922   Sc0000793    43810   42123   52227 Mcavernosa29857    G
## 201  7922   Sc0000793    43810   39677   44813 Mcavernosa29856    G
## 202  8033   Sc0000844    57836   54559   62548 Mcavernosa25609    K
## 203  8114   Sc0000898    50293   48245   61625 Mcavernosa23625    U
## 204  8114   Sc0000898    50293   42504   52009 Mcavernosa23624    Z
## 205  8116   Sc0000898    70539   69193   80640 Mcavernosa23628    S
## 206  8117   Sc0000898    70540   69193   80640 Mcavernosa23628    S
## 207  8147   Sc0000922    80746   73120   82306 Mcavernosa23886    K
## 208  8147   Sc0000922    80746   79221   86885 Mcavernosa23888    O
## 209  8184   Sc0000949    20378   17095   36452 Mcavernosa24064    T
## 210  8390   Sc0001344    10967    5417   11093 Mcavernosa35036    A
## 211  8543 xfSc0000001   269751  267407  300117 Mcavernosa01583 <NA>
## 212  8552 xfSc0000001   911114  881551  913362 Mcavernosa01663    S
## 213  8731 xfSc0000014    17613   11771   20653 Mcavernosa19028 <NA>
## 214  8732 xfSc0000014    17615   11771   20653 Mcavernosa19028 <NA>
## 215  8739 xfSc0000014   180920  172494  188797 Mcavernosa19038 <NA>
## 216  8855 xfSc0000031    98049   66537  100795 Mcavernosa26565    O
## 217  8932 xfSc0000050    38018   35178   45907 Mcavernosa17957    T
## 218  9017 xfSc0000084    65207   61669   68446 Mcavernosa25700    E
## 219  9018 xfSc0000084    65543   65358   76356 Mcavernosa25701    E
## 220  9018 xfSc0000084    65543   61669   68446 Mcavernosa25700    E
## 221  9132 xfSc0000184    33389   33119   58424 Mcavernosa27570    E
## 222  9132 xfSc0000184    33389   24070   34169 Mcavernosa27569    G
## 223  9210 xfSc0000434    19350   18671   39356 Mcavernosa35017    P
## 224  9224 xfSc0000545    18714   16370   25280 Mcavernosa29089 <NA>
## 225  9224 xfSc0000545    18714   10958   20002 Mcavernosa29088 <NA>
## 226  9258 xfSc0000869    10652    4728   10830 Mcavernosa34116    S
## 227  9367 xpSc0004672   137903  117553  138272 Mcavernosa03177    S
## 228  9367 xpSc0004672   137903  134910  152612 Mcavernosa03178    S
## 229  9437 xpSc0004676   333208  320021  334250 Mcavernosa14528 <NA>
## 230  9437 xpSc0004676   333208  332570  349536 Mcavernosa14530 <NA>
## 231  9465 xpSc0004679    77832   74393   86485 Mcavernosa32339    S
## 232  9504 xpSc0004683   101818   93090  104310 Mcavernosa22558    O
## 233  9519 xpSc0004686    56404   50923   60994 Mcavernosa11044 <NA>
## 234  9519 xpSc0004686    56404   55791   64145 Mcavernosa11045 <NA>
## 235  9523 xpSc0004686   106805   93060  125737 Mcavernosa11050 <NA>
## 236  9533 xpSc0004689   110580  107004  116532 Mcavernosa21372 <NA>
## 237  9601 xpSc0004703   137182  125654  146124 Mcavernosa17508    Z
## 238  9644 xpSc0004718    25038   22879   32957 Mcavernosa29682 <NA>
## 239  9648 xpSc0004718   110201  109005  116591 Mcavernosa29689 <NA>
## 240  9722 xpSc0004753    68945   44063   78897 Mcavernosa24038    S
## 241  9723 xpSc0004753    68948   44063   78897 Mcavernosa24038    S
## 242  9745 xpSc0004768    13647   11940   16882 Mcavernosa24254    O
## 243  9806 xpSc0004907    15987   12456   22733 Mcavernosa34943 <NA>
## 244  9806 xpSc0004907    15987    5755   16170 Mcavernosa34942    S
## 245  9807 xpSc0004907    16619   12456   22733 Mcavernosa34943 <NA>
## 246  9893 xpSc0006496     1436    -806    6628 Mcavernosa35153    E
##                                                                                                         protein
## 1                                                                                                       unknown
## 2                                                                                                       unknown
## 3                                                                                                       unknown
## 4                                                                                                       unknown
## 5                                                                                                       unknown
## 6                                                                                                       unknown
## 7                                                                                                       unknown
## 8                                                                                                       unknown
## 9                                                                                                       unknown
## 10                                                                                                         SANT
## 11                                                                          Protein inhibitor of activated STAT
## 12                                                                                                synaptotagmin
## 13                                                                                                      unknown
## 14                                                                                 endoplasmic reticulum lectin
## 15                                                                       Nicotinatenucleotide pyrophosphorylase
## 16                                                                                        TRAF-type zinc finger
## 17                                                                                                      unknown
## 18                                                                                                      unknown
## 19                                                                                                      unknown
## 20                                                                                   Tubulin folding cofactor E
## 21                                                                                                      unknown
## 22                                                                                                      unknown
## 23                                                                                                      unknown
## 24                                                                                                   synthetase
## 25                                                                 3-phosphoadenosine 5-phosphosulfate synthase
## 26                                                                                          Leucine Rich Repeat
## 27                                                                                                      unknown
## 28                                                                                                      unknown
## 29                                                                                              forkhead box L2
## 30                                                                                               meprin A, beta
## 31                                                                                Stromal cell derived factor 4
## 32                                                                                               meprin A, beta
## 33                                                                                Stromal cell derived factor 4
## 34                                                                                    Transmembrane protein 135
## 35                                                                                                      unknown
## 36                                                                                                      unknown
## 37                                                                                            Guanylate cyclase
## 38                                                                                                      unknown
## 39                                                                                                      unknown
## 40                                                                                                      unknown
## 41                                                                                                      unknown
## 42                                                                                                      unknown
## 43                                                                                                      unknown
## 44                                                                                                      unknown
## 45                                                                                                      unknown
## 46                                                                                                      unknown
## 47                                                                        SRY (sex determining region Y)-box 17
## 48                                                                  Tubulin tyrosine ligase-like family, member
## 49                                                          intraflagellar transport 20 homolog (Chlamydomonas)
## 50                                                                                                       Globin
## 51                                                                                                      unknown
## 52                                                                                                     homeobox
## 53                                                                                                      unknown
## 54                                                                                 ADAM metallopeptidase domain
## 55                                                                receptor tyrosine kinase-like orphan receptor
## 56                                                                                         Lectin C-type domain
## 57                                                                                         Lectin C-type domain
## 58                                                                                         Lectin C-type domain
## 59  Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis (By similarity)
## 60  Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis (By similarity)
## 61                                                                                                      unknown
## 62                                                                                                      unknown
## 63                                                                                            Iroquois homeobox
## 64                                                                                                      unknown
## 65                                                                                            Iroquois homeobox
## 66                                                                          solute carrier family 25, member 38
## 67                                                                                                      unknown
## 68                                                                family with sequence similarity 181, member B
## 69                                                                           Diphthamide biosynthesis protein 3
## 70                                                                       Cholinergic receptor, nicotinic, alpha
## 71                                                                              cholinergic receptor, nicotinic
## 72                                                                                                      unknown
## 73                                                     leucine rich repeat and sterile alpha motif containing 1
## 74                                                                            Coiled-coil domain containing 151
## 75                                                                       Cholinergic receptor, nicotinic, alpha
## 76                                                                                                     protease
## 77                                                                ATP-binding cassette sub-family A ABC1 member
## 78                                                                         replication factor C (activator 1) 5
## 79                                                                                                      unknown
## 80                                                                                                      unknown
## 81                                                                                                      unknown
## 82                                                                                                      unknown
## 83                                                                                                      unknown
## 84                                                                          PIKK family atypical protein kinase
## 85                                                                                                      unknown
## 86                                                                                                      unknown
## 87                                                                                                      unknown
## 88                                                                                                      unknown
## 89                                                                                                      unknown
## 90                                                                                                      unknown
## 91                                                                                                      unknown
## 92                                                                                                      unknown
## 93                                                                                                      unknown
## 94                                                                                                      unknown
## 95                                                                                                      unknown
## 96                                                                                                      unknown
## 97                                                                                                      unknown
## 98                                                                                                      unknown
## 99                                                                                          apoptosis inhibitor
## 100                                     Microtubule associated monoxygenase, calponin and LIM domain containing
## 101                                                                              EF-hand calcium binding domain
## 102                                                                                           Guanine deaminase
## 103                                 pleckstrin homology domain containing, family G (with RhoGef domain) member
## 104                                                                                                  synthetase
## 105                                                                          chromosome 2 open reading frame 29
## 106                                                                                                     unknown
## 107                                                                                                     unknown
## 108                                                                                                     unknown
## 109                                                                                                     unknown
## 110                                                                                                     unknown
## 111                                                                                                     unknown
## 112                                                                                                     unknown
## 113                                                                                                     unknown
## 114                                                                                      Zinc finger, C2H2 type
## 115                                                             RNA binding protein, fox-1 homolog (C. elegans)
## 116                                                                             Dermatan sulfate epimerase-like
## 117                                                                                      Lowdensity lipoprotein
## 118                                                                                                     unknown
## 119                                                                                                     unknown
## 120                                                                                                     unknown
## 121                                                                               armadillo repeat containing 2
## 122                                                                                                     unknown
## 123                                                                         chromosome 11 open reading frame 65
## 124                                                                                                     unknown
## 125                                                                                           hephaestin-like 1
## 126                                                                                                     unknown
## 127                                                                                   Transmembrane protein 205
## 128                                                                               Neuronal PAS domain protein 2
## 129                                                                                                     unknown
## 130                                                                                                     unknown
## 131                                 GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein
## 132                                 GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein
## 133                                                                                                     unknown
## 134                                                                                                     unknown
## 135                                                                                                     unknown
## 136                                                                                                     unknown
## 137                                                                                                     unknown
## 138                                                                                              ankyrin repeat
## 139                                                                                           carboxylase, beta
## 140                                  myeloid lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)
## 141                                                                                   Sodium hydrogen exchanger
## 142                                                                                                     unknown
## 143                                                                                                     unknown
## 144                                                                                                     unknown
## 145                                                                                                     unknown
## 146                                                                                                     unknown
## 147                                                                                                     unknown
## 148                                                                                                     unknown
## 149                                                                                                     unknown
## 150                                                                                                     unknown
## 151                                                                                                     unknown
## 152                                                                                                     unknown
## 153                                                                                                     unknown
## 154                                                                                                     unknown
## 155                                                                   iron-responsive element binding protein 2
## 156                                                                                     mannosidase alpha class
## 157                                                                                                     unknown
## 158                                                                                                     unknown
## 159                                                                                         5-3 exoribonuclease
## 160              to signal transducer and activator of transcription interacting protein 1 Hydra magnipapillata
## 161                                                                                                    homeobox
## 162                                                                                                dystrobrevin
## 163                                                                                                    kiaa1958
## 164                                                                                                     unknown
## 165                                                                                          UBX domain protein
## 166                                                                                                     unknown
## 167                                                                                          UBX domain protein
## 168                                                           Dishevelled Associated Activator of Morphogenesis
## 169                                                                 Programmed cell death 6 interacting protein
## 170                                                                                                        MYSc
## 171                                                                CTS telomere maintenance complex component 1
## 172                                                                                                     unknown
## 173                                                                                  Methyltransferase like 21D
## 174                                                                                  protein kinase C substrate
## 175                                                                                                  calmodulin
## 176                                                                                                     unknown
## 177                                                                                                     unknown
## 178                                                                                                     unknown
## 179                                                                                                     unknown
## 180                                                                                                     unknown
## 181                                                                                                     unknown
## 182                                                                                                     unknown
## 183                                                                                                     unknown
## 184                                                                                                     unknown
## 185                                                                                  glutamine amidotransferase
## 186                                                                                                     unknown
## 187                                                                                                     unknown
## 188                                                                                   Polycystic kidney disease
## 189                                                                                                     unknown
## 190                                                                                        DNA polymerase kappa
## 191                                                                                            adenylate kinase
## 192                                                                  protein tyrosine phosphatase receptor type
## 193                                                                                                     unknown
## 194                                                                                TBC1 domain family, member 7
## 195                                                                  nucleolar and spindle associated protein 1
## 196                                                                                                     unknown
## 197                                                                                            Carboxypeptidase
## 198                                                             Major facilitator superfamily domain containing
## 199                                                                                                     unknown
## 200                                                                                                   Aquaporin
## 201                                                                                                   Aquaporin
## 202                                                                                                UNC homeobox
## 203                                                                            RAB14 member RAS oncogene family
## 204                                                                                            (actinin), alpha
## 205                                                                       BRO1 domain and CAAX motif containing
## 206                                                                       BRO1 domain and CAAX motif containing
## 207                                                                                Polycomb group ring finger 1
## 208                                                             Inherit from opiNOG: Polycomb group ring finger
## 209                                                                                           Guanylate cyclase
## 210                                                                            wilms tumor 1 associated protein
## 211                                                                                                     unknown
## 212                                                                       Ral GTPase-activating protein subunit
## 213                                                                                                     unknown
## 214                                                                                                     unknown
## 215                                                                                                     unknown
## 216                                                      ADAM metallopeptidase with thrombospondin type 1 motif
## 217                  Ligand for members of the frizzled family of seven transmembrane receptors (By similarity)
## 218                                                                            Inherit from COG: oxidoreductase
## 219                                                                            Inherit from COG: oxidoreductase
## 220                                                                            Inherit from COG: oxidoreductase
## 221                                                                                        cysteine desulfurase
## 222                                                                            solute carrier family 16, member
## 223                                                                                            chloride channel
## 224                                                                                                     unknown
## 225                                                                                                     unknown
## 226                                                                                                     unknown
## 227                                                                                                     unknown
## 228                                                                                                     unknown
## 229                                                                                                     unknown
## 230                                                                                                     unknown
## 231                                                                                               storkhead box
## 232                                                                  Protein-l-isoaspartate O-methyltransferase
## 233                                                                                                     unknown
## 234                                                                                                     unknown
## 235                                                                                                     unknown
## 236                                                                                                     unknown
## 237                                                                                            (actinin), alpha
## 238                                                                                                     unknown
## 239                                                                                                     unknown
## 240                                                                        Chromosome 14 open reading frame 159
## 241                                                                        Chromosome 14 open reading frame 159
## 242                                                     ADAM metallopeptidase with thrombospondin type 1, motif
## 243                                                                                                     unknown
## 244                                                                                 SPFH domain / Band 7 family
## 245                                                                                                     unknown
## 246                                                                                              L-asparaginase
#only show annotated genes
outsAnno = outsByGene %>% filter(protein != "unknown")
outsAnno
##     locus      chromo position   start     end            gene  cog
## 1     355   Sc0000007   832690  823671  835359 Mcavernosa00064    B
## 2     356   Sc0000007   880296  878147  888205 Mcavernosa00072    K
## 3     368   Sc0000007  1337188 1330506 1340868 Mcavernosa00118 T, U
## 4     372   Sc0000008    58676   56915   71673 Mcavernosa00135    O
## 5     372   Sc0000008    58676   55911   60813 Mcavernosa00134    F
## 6     386   Sc0000008   503055  492721  503102 Mcavernosa00187    O
## 7     632   Sc0000015   159724  145156  161161 Mcavernosa01022    O
## 8     788   Sc0000019   442489  438004  446586 Mcavernosa01737    I
## 9     793   Sc0000019   706060  700863  720685 Mcavernosa01750    F
## 10    885   Sc0000022   239151  237450  248306 Mcavernosa01985    T
## 11    994   Sc0000025   275188  273853  278737 Mcavernosa03361    K
## 12   1003   Sc0000025   482056  472108  487567 Mcavernosa03375    O
## 13   1003   Sc0000025   482056  480195  487577 Mcavernosa03377    O
## 14   1004   Sc0000025   482065  472108  487567 Mcavernosa03375    O
## 15   1004   Sc0000025   482065  480195  487577 Mcavernosa03377    O
## 16   1073   Sc0000028   801272  800600  817320 Mcavernosa03681    K
## 17   1290   Sc0000035   241187  216273  248825 Mcavernosa07247    T
## 18   1602   Sc0000048   780568  776755  781852 Mcavernosa24579    K
## 19   1621   Sc0000049   677814  676938  691658 Mcavernosa24636    O
## 20   1641   Sc0000050   345719  339508  345869 Mcavernosa24682    U
## 21   1641   Sc0000050   345719  343656  351153 Mcavernosa24683    S
## 22   1733   Sc0000053   657280  651154  661769 Mcavernosa24928    K
## 23   1918   Sc0000062    38808   26976   48049 Mcavernosa16630    O
## 24   1925   Sc0000062   295853  281605  298921 Mcavernosa16657    T
## 25   2025   Sc0000066   650888  644107  676724 Mcavernosa16979    S
## 26   2026   Sc0000066   652197  644107  676724 Mcavernosa16979    S
## 27   2027   Sc0000066   654108  644107  676724 Mcavernosa16979    S
## 28   2042   Sc0000067   284567  278061  285961 Mcavernosa17017    P
## 29   2042   Sc0000067   284567  282441  289151 Mcavernosa17018    P
## 30   2091   Sc0000069   259168  250294  259857 Mcavernosa17169    K
## 31   2092   Sc0000069   259171  250294  259857 Mcavernosa17169    K
## 32   2245   Sc0000075   616525  607578  618954 Mcavernosa02407    C
## 33   2304   Sc0000078   538250  533613  551888 Mcavernosa02598    O
## 34   2307   Sc0000078   614585  613259  619758 Mcavernosa02606    L
## 35   2311   Sc0000079   250813  238726  255446 Mcavernosa02643    T
## 36   2311   Sc0000079   250813  248660  262153 Mcavernosa02644    T
## 37   2349   Sc0000080   361792  360415  371754 Mcavernosa02783    T
## 38   2353   Sc0000080   488331  487227  499585 Mcavernosa02799    S
## 39   2379   Sc0000082    92075   81308   92957 Mcavernosa02895    T
## 40   2379   Sc0000082    92075   90633  109672 Mcavernosa02896    O
## 41   2411   Sc0000084    35373   33192   72247 Mcavernosa03031    Q
## 42   2470   Sc0000088   271450  264057  273126 Mcavernosa30892    L
## 43   2871   Sc0000110   465061  459333  473275 Mcavernosa04749    L
## 44   3396   Sc0000143   233814  224785  238979 Mcavernosa12556    T
## 45   3605   Sc0000156   233175  232263  242297 Mcavernosa13321    Z
## 46   3687   Sc0000162   271434  263202  272051 Mcavernosa13626 T, U
## 47   3697   Sc0000163   156786  154135  178495 Mcavernosa13675    F
## 48   3702   Sc0000163   476311  449149  476793 Mcavernosa13698    T
## 49   3731   Sc0000165    41199   36908   45903 Mcavernosa13845    I
## 50   3732   Sc0000165   109520  101511  128726 Mcavernosa13852    L
## 51   4323   Sc0000203   157445  155494  167885 Mcavernosa08740    K
## 52   4402   Sc0000209   350281  347785  365259 Mcavernosa09014    A
## 53   4404   Sc0000210   164055  158822  165206 Mcavernosa09023    O
## 54   4489   Sc0000216   311217  285965  314077 Mcavernosa14323    T
## 55   4538   Sc0000221   445181  420545  445853 Mcavernosa14579 T, W
## 56   4538   Sc0000221   445181  443025  456073 Mcavernosa14581    S
## 57   4612   Sc0000227   405468  401584  406889 Mcavernosa14838    Q
## 58   4654   Sc0000230   214219  210931  218813 Mcavernosa14928    S
## 59   4684   Sc0000232   390834  379259  409857 Mcavernosa15121    K
## 60   4885   Sc0000246   158533  150339  165139 Mcavernosa11524    O
## 61   4886   Sc0000246   160029  150339  165139 Mcavernosa11524    O
## 62   5203   Sc0000274   356889  326224  356983 Mcavernosa31974    T
## 63   5244   Sc0000280   366163  364767  372154 Mcavernosa32117 E, I
## 64   5264   Sc0000284   186309  183546  206825 Mcavernosa32213    S
## 65   5287   Sc0000287   272412  265916  289527 Mcavernosa32317    P
## 66   5760   Sc0000345   152147  147574  158683 Mcavernosa19881 A, J
## 67   5769   Sc0000346    94998   93359   99925 Mcavernosa19908    G
## 68   5801   Sc0000350   197049  196914  207639 Mcavernosa20016    A
## 69   5842   Sc0000354   127506  126707  132765 Mcavernosa21924 B, K
## 70   5842   Sc0000354   127506  121023  128066 Mcavernosa21923    K
## 71   5971   Sc0000370   209590  206117  245168 Mcavernosa22382    Z
## 72   6040   Sc0000382   126036  124404  130113 Mcavernosa22726    S
## 73   6068   Sc0000386   218550  216541  229696 Mcavernosa15423    O
## 74   6070   Sc0000386   218553  216541  229696 Mcavernosa15423    O
## 75   6095   Sc0000389   100840   85399  108688 Mcavernosa15490 T, Z
## 76   6106   Sc0000390    96448   92122  109465 Mcavernosa15521    S
## 77   6132   Sc0000392   276515  262325  278763 Mcavernosa15635    Z
## 78   6138   Sc0000395    53353   48635   58418 Mcavernosa15712    S
## 79   6170   Sc0000398   209284  208874  217574 Mcavernosa15811    A
## 80   6170   Sc0000398   209284  203599  212365 Mcavernosa15810    T
## 81   6191   Sc0000401    73136   69814   86271 Mcavernosa15895    T
## 82   6671   Sc0000478    84729   81991   86752 Mcavernosa09719    F
## 83   7088   Sc0000564    41161   40367   46799 Mcavernosa26807 P, T
## 84   7146   Sc0000576   103072  100970  107264 Mcavernosa27004    L
## 85   7191   Sc0000586    61007   54497   64743 Mcavernosa20087    F
## 86   7235   Sc0000596   132906  131076  168692 Mcavernosa20343    T
## 87   7650   Sc0000680   151817  149039  155842 Mcavernosa18111    S
## 88   7661   Sc0000682   137909  127400  138441 Mcavernosa18143    S
## 89   7689   Sc0000691    93534   87294   99827 Mcavernosa22890    E
## 90   7749   Sc0000713   106608  105346  111221 Mcavernosa23168    G
## 91   7922   Sc0000793    43810   42123   52227 Mcavernosa29857    G
## 92   7922   Sc0000793    43810   39677   44813 Mcavernosa29856    G
## 93   8033   Sc0000844    57836   54559   62548 Mcavernosa25609    K
## 94   8114   Sc0000898    50293   48245   61625 Mcavernosa23625    U
## 95   8114   Sc0000898    50293   42504   52009 Mcavernosa23624    Z
## 96   8116   Sc0000898    70539   69193   80640 Mcavernosa23628    S
## 97   8117   Sc0000898    70540   69193   80640 Mcavernosa23628    S
## 98   8147   Sc0000922    80746   73120   82306 Mcavernosa23886    K
## 99   8147   Sc0000922    80746   79221   86885 Mcavernosa23888    O
## 100  8184   Sc0000949    20378   17095   36452 Mcavernosa24064    T
## 101  8390   Sc0001344    10967    5417   11093 Mcavernosa35036    A
## 102  8552 xfSc0000001   911114  881551  913362 Mcavernosa01663    S
## 103  8855 xfSc0000031    98049   66537  100795 Mcavernosa26565    O
## 104  8932 xfSc0000050    38018   35178   45907 Mcavernosa17957    T
## 105  9017 xfSc0000084    65207   61669   68446 Mcavernosa25700    E
## 106  9018 xfSc0000084    65543   65358   76356 Mcavernosa25701    E
## 107  9018 xfSc0000084    65543   61669   68446 Mcavernosa25700    E
## 108  9132 xfSc0000184    33389   33119   58424 Mcavernosa27570    E
## 109  9132 xfSc0000184    33389   24070   34169 Mcavernosa27569    G
## 110  9210 xfSc0000434    19350   18671   39356 Mcavernosa35017    P
## 111  9465 xpSc0004679    77832   74393   86485 Mcavernosa32339    S
## 112  9504 xpSc0004683   101818   93090  104310 Mcavernosa22558    O
## 113  9601 xpSc0004703   137182  125654  146124 Mcavernosa17508    Z
## 114  9722 xpSc0004753    68945   44063   78897 Mcavernosa24038    S
## 115  9723 xpSc0004753    68948   44063   78897 Mcavernosa24038    S
## 116  9745 xpSc0004768    13647   11940   16882 Mcavernosa24254    O
## 117  9806 xpSc0004907    15987    5755   16170 Mcavernosa34942    S
## 118  9893 xpSc0006496     1436    -806    6628 Mcavernosa35153    E
##                                                                                                         protein
## 1                                                                                                          SANT
## 2                                                                           Protein inhibitor of activated STAT
## 3                                                                                                 synaptotagmin
## 4                                                                                  endoplasmic reticulum lectin
## 5                                                                        Nicotinatenucleotide pyrophosphorylase
## 6                                                                                         TRAF-type zinc finger
## 7                                                                                    Tubulin folding cofactor E
## 8                                                                                                    synthetase
## 9                                                                  3-phosphoadenosine 5-phosphosulfate synthase
## 10                                                                                          Leucine Rich Repeat
## 11                                                                                              forkhead box L2
## 12                                                                                               meprin A, beta
## 13                                                                                Stromal cell derived factor 4
## 14                                                                                               meprin A, beta
## 15                                                                                Stromal cell derived factor 4
## 16                                                                                    Transmembrane protein 135
## 17                                                                                            Guanylate cyclase
## 18                                                                        SRY (sex determining region Y)-box 17
## 19                                                                  Tubulin tyrosine ligase-like family, member
## 20                                                          intraflagellar transport 20 homolog (Chlamydomonas)
## 21                                                                                                       Globin
## 22                                                                                                     homeobox
## 23                                                                                 ADAM metallopeptidase domain
## 24                                                                receptor tyrosine kinase-like orphan receptor
## 25                                                                                         Lectin C-type domain
## 26                                                                                         Lectin C-type domain
## 27                                                                                         Lectin C-type domain
## 28  Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis (By similarity)
## 29  Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis (By similarity)
## 30                                                                                            Iroquois homeobox
## 31                                                                                            Iroquois homeobox
## 32                                                                          solute carrier family 25, member 38
## 33                                                                family with sequence similarity 181, member B
## 34                                                                           Diphthamide biosynthesis protein 3
## 35                                                                       Cholinergic receptor, nicotinic, alpha
## 36                                                                              cholinergic receptor, nicotinic
## 37                                                     leucine rich repeat and sterile alpha motif containing 1
## 38                                                                            Coiled-coil domain containing 151
## 39                                                                       Cholinergic receptor, nicotinic, alpha
## 40                                                                                                     protease
## 41                                                                ATP-binding cassette sub-family A ABC1 member
## 42                                                                         replication factor C (activator 1) 5
## 43                                                                          PIKK family atypical protein kinase
## 44                                                                                          apoptosis inhibitor
## 45                                      Microtubule associated monoxygenase, calponin and LIM domain containing
## 46                                                                               EF-hand calcium binding domain
## 47                                                                                            Guanine deaminase
## 48                                  pleckstrin homology domain containing, family G (with RhoGef domain) member
## 49                                                                                                   synthetase
## 50                                                                           chromosome 2 open reading frame 29
## 51                                                                                       Zinc finger, C2H2 type
## 52                                                              RNA binding protein, fox-1 homolog (C. elegans)
## 53                                                                              Dermatan sulfate epimerase-like
## 54                                                                                       Lowdensity lipoprotein
## 55                                                                                armadillo repeat containing 2
## 56                                                                          chromosome 11 open reading frame 65
## 57                                                                                            hephaestin-like 1
## 58                                                                                    Transmembrane protein 205
## 59                                                                                Neuronal PAS domain protein 2
## 60                                  GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein
## 61                                  GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein
## 62                                                                                               ankyrin repeat
## 63                                                                                            carboxylase, beta
## 64                                   myeloid lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)
## 65                                                                                    Sodium hydrogen exchanger
## 66                                                                    iron-responsive element binding protein 2
## 67                                                                                      mannosidase alpha class
## 68                                                                                          5-3 exoribonuclease
## 69               to signal transducer and activator of transcription interacting protein 1 Hydra magnipapillata
## 70                                                                                                     homeobox
## 71                                                                                                 dystrobrevin
## 72                                                                                                     kiaa1958
## 73                                                                                           UBX domain protein
## 74                                                                                           UBX domain protein
## 75                                                            Dishevelled Associated Activator of Morphogenesis
## 76                                                                  Programmed cell death 6 interacting protein
## 77                                                                                                         MYSc
## 78                                                                 CTS telomere maintenance complex component 1
## 79                                                                                   Methyltransferase like 21D
## 80                                                                                   protein kinase C substrate
## 81                                                                                                   calmodulin
## 82                                                                                   glutamine amidotransferase
## 83                                                                                    Polycystic kidney disease
## 84                                                                                         DNA polymerase kappa
## 85                                                                                             adenylate kinase
## 86                                                                   protein tyrosine phosphatase receptor type
## 87                                                                                 TBC1 domain family, member 7
## 88                                                                   nucleolar and spindle associated protein 1
## 89                                                                                             Carboxypeptidase
## 90                                                              Major facilitator superfamily domain containing
## 91                                                                                                    Aquaporin
## 92                                                                                                    Aquaporin
## 93                                                                                                 UNC homeobox
## 94                                                                             RAB14 member RAS oncogene family
## 95                                                                                             (actinin), alpha
## 96                                                                        BRO1 domain and CAAX motif containing
## 97                                                                        BRO1 domain and CAAX motif containing
## 98                                                                                 Polycomb group ring finger 1
## 99                                                              Inherit from opiNOG: Polycomb group ring finger
## 100                                                                                           Guanylate cyclase
## 101                                                                            wilms tumor 1 associated protein
## 102                                                                       Ral GTPase-activating protein subunit
## 103                                                      ADAM metallopeptidase with thrombospondin type 1 motif
## 104                  Ligand for members of the frizzled family of seven transmembrane receptors (By similarity)
## 105                                                                            Inherit from COG: oxidoreductase
## 106                                                                            Inherit from COG: oxidoreductase
## 107                                                                            Inherit from COG: oxidoreductase
## 108                                                                                        cysteine desulfurase
## 109                                                                            solute carrier family 16, member
## 110                                                                                            chloride channel
## 111                                                                                               storkhead box
## 112                                                                  Protein-l-isoaspartate O-methyltransferase
## 113                                                                                            (actinin), alpha
## 114                                                                        Chromosome 14 open reading frame 159
## 115                                                                        Chromosome 14 open reading frame 159
## 116                                                     ADAM metallopeptidase with thrombospondin type 1, motif
## 117                                                                                 SPFH domain / Band 7 family
## 118                                                                                              L-asparaginase
#df_uniq <- unique(outsAnno$locus)
#length(df_uniq)

write.csv(x=outsAnno, file="annotatedOutliers.csv")
source('plot_R.r')

dat = read.table("fkMcav.baye_fst.txt",header=T)
head(dat)
##       prob  log10.PO.     qval     alpha      fst
## 1 0.117624   -0.87516 0.675734 -0.100360 0.027392
## 2 0.077215   -1.07740 0.835710 -0.036717 0.028434
## 3 0.071014   -1.11670 0.853910 -0.017603 0.028814
## 4 1.000000 1000.00000 0.000000  1.625500 0.131590
## 5 0.076215   -1.08350 0.839110 -0.025847 0.028704
## 6 0.082216   -1.04780 0.819380  0.033438 0.030727
table(dat[,"qval"]<0.01)
## 
## FALSE  TRUE 
##  9767   139
highOuts=which(dat[,"qval"]<0.01)
plot_bayescan("fkMcav.baye_fst.txt",FDR=0.01,add_text=F,size=0.5,highlight=highOuts)

## $outliers
##   [1]    4   79  191  266  356  368  386  498  547  571  619  672  703  759  776  799
##  [17]  885  904  955  994 1290 1320 1421 1603 1621 1641 1658 1716 1822 2004 2025 2042
##  [33] 2048 2092 2174 2257 2269 2307 2349 2411 2436 2438 2439 2576 2595 2639 2891 2905
##  [49] 2989 3009 3060 3097 3135 3136 3212 3244 3605 3687 3702 3876 4280 4323 4489 4538
##  [65] 4612 4623 4654 4703 4734 4817 4961 5040 5166 5393 5424 5441 5469 5476 5509 5512
##  [81] 5577 5611 5705 5780 5971 6042 6144 6191 6465 6573 6612 6679 6812 6886 6893 7111
##  [97] 7276 7403 7411 7607 7650 7661 7681 7689 7787 8033 8049 8116 8117 8227 8261 8262
## [113] 8390 8490 8496 8611 8731 8732 8739 8855 8858 8872 9160 9224 9364 9367 9457 9458
## [129] 9465 9519 9523 9533 9648 9722 9723 9725 9745 9807 9810
## 
## $nb_outliers
## [1] 139
genes = read.table("mcav_gene_regions.tab")
names(genes) = c("chromo","start","end","gene")

# expand gene regions ± 2000 bp
genes$start = genes$start -2000
genes$end = genes$end +2000

gnames = read.table("mcav_cog.txt", sep = "\t")
names(gnames) = c("gene", "cog", "protein")

genes = full_join(genes, gnames, by = "gene")
genes$protein=as.character(genes$protein)
genes$protein[is.na(genes$protein)]="unknown"

#how many annotated genes do we have?
nrow(genes[genes$protein!="unknown",])
## [1] 9912
head(genes)
##      chromo  start    end            gene  cog
## 1 Sc0000101  17738  46551 Mcavernosa04235 <NA>
## 2 Sc0000101 113438 122548 Mcavernosa04241 <NA>
## 3 Sc0000101 105283 117140 Mcavernosa04239 <NA>
## 4 Sc0000101 182029 186424 Mcavernosa04243    F
## 5 Sc0000101 118230 122978 Mcavernosa04242 <NA>
## 6 Sc0000101 104867 111016 Mcavernosa04238    L
##                                                    protein
## 1                                                  unknown
## 2                                                  unknown
## 3                                                  unknown
## 4                                         (dCMP) deaminase
## 5                                                  unknown
## 6 Inherit from meNOG: multicellular organismal development
snpLoci = read.table("fkMcavNoClones.mafs.gz", header = TRUE)
snpLoci$locus = c(1:nrow(snpLoci))

highOutsByGene = snpLoci %>% dplyr::select(locus, chromo, position) %>% 
  filter(locus %in% highOuts) %>%
  full_join(., genes, by = "chromo") %>% 
  filter(position>start, position<end)

highOutsByGene
##    locus      chromo position   start     end            gene  cog
## 1      4   Sc0000000   133071  132438  155504 Mcavernosa06199 <NA>
## 2    191   Sc0000003  1236302 1231990 1241385 Mcavernosa06771 <NA>
## 3    266   Sc0000005   415610  413324  422027 Mcavernosa06992 <NA>
## 4    356   Sc0000007   880296  878147  888205 Mcavernosa00072    K
## 5    368   Sc0000007  1337188 1330506 1340868 Mcavernosa00118 T, U
## 6    386   Sc0000008   503055  492721  503102 Mcavernosa00187    O
## 7    386   Sc0000008   503055  502715  507847 Mcavernosa00189 <NA>
## 8    386   Sc0000008   503055  501330  506280 Mcavernosa00188 <NA>
## 9    547   Sc0000012    48483   47025   51570 Mcavernosa00675 <NA>
## 10   759   Sc0000018   792663  771401  794949 Mcavernosa01502 <NA>
## 11   776   Sc0000019   161993  160590  169407 Mcavernosa01711    S
## 12   885   Sc0000022   239151  237450  248306 Mcavernosa01985    T
## 13   904   Sc0000022   699099  696305  710712 Mcavernosa02040 <NA>
## 14   955   Sc0000024   279084  277990  287503 Mcavernosa03257 <NA>
## 15   994   Sc0000025   275188  273853  278737 Mcavernosa03361    K
## 16  1290   Sc0000035   241187  216273  248825 Mcavernosa07247    T
## 17  1421   Sc0000041   414834  387188  417847 Mcavernosa07881 <NA>
## 18  1421   Sc0000041   414834  411811  421571 Mcavernosa07882 <NA>
## 19  1621   Sc0000049   677814  676938  691658 Mcavernosa24636    O
## 20  1641   Sc0000050   345719  339508  345869 Mcavernosa24682    U
## 21  1641   Sc0000050   345719  343656  351153 Mcavernosa24683    S
## 22  2025   Sc0000066   650888  644107  676724 Mcavernosa16979    S
## 23  2042   Sc0000067   284567  278061  285961 Mcavernosa17017    P
## 24  2042   Sc0000067   284567  282441  289151 Mcavernosa17018    P
## 25  2092   Sc0000069   259171  255860  261193 Mcavernosa17170 <NA>
## 26  2092   Sc0000069   259171  250294  259857 Mcavernosa17169    K
## 27  2269   Sc0000077   132592  126071  206963 Mcavernosa02504    S
## 28  2307   Sc0000078   614585  613259  619758 Mcavernosa02606    L
## 29  2349   Sc0000080   361792  358370  363365 Mcavernosa02782 <NA>
## 30  2349   Sc0000080   361792  360415  371754 Mcavernosa02783    T
## 31  2411   Sc0000084    35373   33192   72247 Mcavernosa03031    Q
## 32  2639   Sc0000097   272642  263264  286159 Mcavernosa31430 <NA>
## 33  2905   Sc0000114    15141    3350   16689 Mcavernosa04908 <NA>
## 34  2989   Sc0000119   156354  152125  158165 Mcavernosa05289 <NA>
## 35  3009   Sc0000120   193690  181368  195746 Mcavernosa05341 <NA>
## 36  3097   Sc0000125    30700   30571   35101 Mcavernosa05607 <NA>
## 37  3135   Sc0000127    94790   88800  100135 Mcavernosa05715 <NA>
## 38  3212   Sc0000131   100946   93463  119509 Mcavernosa05895 <NA>
## 39  3605   Sc0000156   233175  232263  242297 Mcavernosa13321    Z
## 40  3687   Sc0000162   271434  263202  272051 Mcavernosa13626 T, U
## 41  3702   Sc0000163   476311  449149  476793 Mcavernosa13698    T
## 42  3876   Sc0000173   294276  269015  303285 Mcavernosa14217 <NA>
## 43  4280   Sc0000200   295534  286186  309693 Mcavernosa08605 <NA>
## 44  4323   Sc0000203   157445  155494  167885 Mcavernosa08740    K
## 45  4489   Sc0000216   311217  285965  314077 Mcavernosa14323    T
## 46  4538   Sc0000221   445181  420545  445853 Mcavernosa14579 T, W
## 47  4538   Sc0000221   445181  423988  445704 Mcavernosa14580 <NA>
## 48  4538   Sc0000221   445181  443025  456073 Mcavernosa14581    S
## 49  4612   Sc0000227   405468  401584  406889 Mcavernosa14838    Q
## 50  4623   Sc0000228   430154  428072  434242 Mcavernosa14875 <NA>
## 51  4654   Sc0000230   214219  210931  218813 Mcavernosa14928    S
## 52  4703   Sc0000233   271811  265838  278226 Mcavernosa15141 <NA>
## 53  5040   Sc0000260   319736  319323  346737 Mcavernosa12107 <NA>
## 54  5393   Sc0000299    46600   38716   47500 Mcavernosa18484 <NA>
## 55  5441   Sc0000303    73881   66298   83229 Mcavernosa18619 <NA>
## 56  5476   Sc0000306   296046  276974  304185 Mcavernosa18753 <NA>
## 57  5509   Sc0000311   306679  301233  311954 Mcavernosa18887 <NA>
## 58  5577   Sc0000319   319167  310661  330433 Mcavernosa19142 <NA>
## 59  5611   Sc0000327    38091   23293   42444 Mcavernosa19334 <NA>
## 60  5705   Sc0000336   232381  225498  234939 Mcavernosa19631 <NA>
## 61  5780   Sc0000347   151002  149194  159410 Mcavernosa19943 <NA>
## 62  5971   Sc0000370   209590  206117  245168 Mcavernosa22382    Z
## 63  6144   Sc0000395   228985  227146  239730 Mcavernosa15724    S
## 64  6191   Sc0000401    73136   69814   86271 Mcavernosa15895    T
## 65  6465   Sc0000443    56694   52892   66115 Mcavernosa10901 <NA>
## 66  6573   Sc0000461    78244   76666   84641 Mcavernosa09358 <NA>
## 67  6573   Sc0000461    78244   65552   79875 Mcavernosa09357 <NA>
## 68  6612   Sc0000465   102579   87010  114820 Mcavernosa09451 <NA>
## 69  7111   Sc0000568    75761   73400   77942 Mcavernosa26898 <NA>
## 70  7650   Sc0000680   151817  149039  155842 Mcavernosa18111    S
## 71  7661   Sc0000682   137909  127400  138441 Mcavernosa18143    S
## 72  7681   Sc0000686   120700  116433  126374 Mcavernosa22820 <NA>
## 73  7689   Sc0000691    93534   87294   99827 Mcavernosa22890    E
## 74  7787   Sc0000730    61782   58333   64367 Mcavernosa23327 <NA>
## 75  8033   Sc0000844    57836   54559   62548 Mcavernosa25609    K
## 76  8116   Sc0000898    70539   69193   80640 Mcavernosa23628    S
## 77  8117   Sc0000898    70540   69193   80640 Mcavernosa23628    S
## 78  8390   Sc0001344    10967    5417   11093 Mcavernosa35036    A
## 79  8731 xfSc0000014    17613   11771   20653 Mcavernosa19028 <NA>
## 80  8732 xfSc0000014    17615   11771   20653 Mcavernosa19028 <NA>
## 81  8739 xfSc0000014   180920  172494  188797 Mcavernosa19038 <NA>
## 82  8855 xfSc0000031    98049   66537  100795 Mcavernosa26565    O
## 83  9224 xfSc0000545    18714   16370   25280 Mcavernosa29089 <NA>
## 84  9224 xfSc0000545    18714   10958   20002 Mcavernosa29088 <NA>
## 85  9367 xpSc0004672   137903  117553  138272 Mcavernosa03177    S
## 86  9367 xpSc0004672   137903  134910  152612 Mcavernosa03178    S
## 87  9465 xpSc0004679    77832   74393   86485 Mcavernosa32339    S
## 88  9519 xpSc0004686    56404   50923   60994 Mcavernosa11044 <NA>
## 89  9519 xpSc0004686    56404   55791   64145 Mcavernosa11045 <NA>
## 90  9523 xpSc0004686   106805   93060  125737 Mcavernosa11050 <NA>
## 91  9533 xpSc0004689   110580  107004  116532 Mcavernosa21372 <NA>
## 92  9648 xpSc0004718   110201  109005  116591 Mcavernosa29689 <NA>
## 93  9722 xpSc0004753    68945   44063   78897 Mcavernosa24038    S
## 94  9723 xpSc0004753    68948   44063   78897 Mcavernosa24038    S
## 95  9745 xpSc0004768    13647   11940   16882 Mcavernosa24254    O
## 96  9807 xpSc0004907    16619   12456   22733 Mcavernosa34943 <NA>
##                                                                                                        protein
## 1                                                                                                      unknown
## 2                                                                                                      unknown
## 3                                                                                                      unknown
## 4                                                                          Protein inhibitor of activated STAT
## 5                                                                                                synaptotagmin
## 6                                                                                        TRAF-type zinc finger
## 7                                                                                                      unknown
## 8                                                                                                      unknown
## 9                                                                                                      unknown
## 10                                                                                                     unknown
## 11                                                                                                     unknown
## 12                                                                                         Leucine Rich Repeat
## 13                                                                                                     unknown
## 14                                                                                                     unknown
## 15                                                                                             forkhead box L2
## 16                                                                                           Guanylate cyclase
## 17                                                                                                     unknown
## 18                                                                                                     unknown
## 19                                                                 Tubulin tyrosine ligase-like family, member
## 20                                                         intraflagellar transport 20 homolog (Chlamydomonas)
## 21                                                                                                      Globin
## 22                                                                                        Lectin C-type domain
## 23 Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis (By similarity)
## 24 Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis (By similarity)
## 25                                                                                                     unknown
## 26                                                                                           Iroquois homeobox
## 27                                                                                                     unknown
## 28                                                                          Diphthamide biosynthesis protein 3
## 29                                                                                                     unknown
## 30                                                    leucine rich repeat and sterile alpha motif containing 1
## 31                                                               ATP-binding cassette sub-family A ABC1 member
## 32                                                                                                     unknown
## 33                                                                                                     unknown
## 34                                                                                                     unknown
## 35                                                                                                     unknown
## 36                                                                                                     unknown
## 37                                                                                                     unknown
## 38                                                                                                     unknown
## 39                                     Microtubule associated monoxygenase, calponin and LIM domain containing
## 40                                                                              EF-hand calcium binding domain
## 41                                 pleckstrin homology domain containing, family G (with RhoGef domain) member
## 42                                                                                                     unknown
## 43                                                                                                     unknown
## 44                                                                                      Zinc finger, C2H2 type
## 45                                                                                      Lowdensity lipoprotein
## 46                                                                               armadillo repeat containing 2
## 47                                                                                                     unknown
## 48                                                                         chromosome 11 open reading frame 65
## 49                                                                                           hephaestin-like 1
## 50                                                                                                     unknown
## 51                                                                                   Transmembrane protein 205
## 52                                                                                                     unknown
## 53                                                                                                     unknown
## 54                                                                                                     unknown
## 55                                                                                                     unknown
## 56                                                                                                     unknown
## 57                                                                                                     unknown
## 58                                                                                                     unknown
## 59                                                                                                     unknown
## 60                                                                                                     unknown
## 61                                                                                                     unknown
## 62                                                                                                dystrobrevin
## 63                                                                                                     unknown
## 64                                                                                                  calmodulin
## 65                                                                                                     unknown
## 66                                                                                                     unknown
## 67                                                                                                     unknown
## 68                                                                                                     unknown
## 69                                                                                                     unknown
## 70                                                                                TBC1 domain family, member 7
## 71                                                                  nucleolar and spindle associated protein 1
## 72                                                                                                     unknown
## 73                                                                                            Carboxypeptidase
## 74                                                                                                     unknown
## 75                                                                                                UNC homeobox
## 76                                                                       BRO1 domain and CAAX motif containing
## 77                                                                       BRO1 domain and CAAX motif containing
## 78                                                                            wilms tumor 1 associated protein
## 79                                                                                                     unknown
## 80                                                                                                     unknown
## 81                                                                                                     unknown
## 82                                                      ADAM metallopeptidase with thrombospondin type 1 motif
## 83                                                                                                     unknown
## 84                                                                                                     unknown
## 85                                                                                                     unknown
## 86                                                                                                     unknown
## 87                                                                                               storkhead box
## 88                                                                                                     unknown
## 89                                                                                                     unknown
## 90                                                                                                     unknown
## 91                                                                                                     unknown
## 92                                                                                                     unknown
## 93                                                                        Chromosome 14 open reading frame 159
## 94                                                                        Chromosome 14 open reading frame 159
## 95                                                     ADAM metallopeptidase with thrombospondin type 1, motif
## 96                                                                                                     unknown
#only show annotated genes
highOutsAnno = highOutsByGene %>% filter(protein != "unknown")
highOutsAnno
##    locus      chromo position   start     end            gene  cog
## 1    356   Sc0000007   880296  878147  888205 Mcavernosa00072    K
## 2    368   Sc0000007  1337188 1330506 1340868 Mcavernosa00118 T, U
## 3    386   Sc0000008   503055  492721  503102 Mcavernosa00187    O
## 4    885   Sc0000022   239151  237450  248306 Mcavernosa01985    T
## 5    994   Sc0000025   275188  273853  278737 Mcavernosa03361    K
## 6   1290   Sc0000035   241187  216273  248825 Mcavernosa07247    T
## 7   1621   Sc0000049   677814  676938  691658 Mcavernosa24636    O
## 8   1641   Sc0000050   345719  339508  345869 Mcavernosa24682    U
## 9   1641   Sc0000050   345719  343656  351153 Mcavernosa24683    S
## 10  2025   Sc0000066   650888  644107  676724 Mcavernosa16979    S
## 11  2042   Sc0000067   284567  278061  285961 Mcavernosa17017    P
## 12  2042   Sc0000067   284567  282441  289151 Mcavernosa17018    P
## 13  2092   Sc0000069   259171  250294  259857 Mcavernosa17169    K
## 14  2307   Sc0000078   614585  613259  619758 Mcavernosa02606    L
## 15  2349   Sc0000080   361792  360415  371754 Mcavernosa02783    T
## 16  2411   Sc0000084    35373   33192   72247 Mcavernosa03031    Q
## 17  3605   Sc0000156   233175  232263  242297 Mcavernosa13321    Z
## 18  3687   Sc0000162   271434  263202  272051 Mcavernosa13626 T, U
## 19  3702   Sc0000163   476311  449149  476793 Mcavernosa13698    T
## 20  4323   Sc0000203   157445  155494  167885 Mcavernosa08740    K
## 21  4489   Sc0000216   311217  285965  314077 Mcavernosa14323    T
## 22  4538   Sc0000221   445181  420545  445853 Mcavernosa14579 T, W
## 23  4538   Sc0000221   445181  443025  456073 Mcavernosa14581    S
## 24  4612   Sc0000227   405468  401584  406889 Mcavernosa14838    Q
## 25  4654   Sc0000230   214219  210931  218813 Mcavernosa14928    S
## 26  5971   Sc0000370   209590  206117  245168 Mcavernosa22382    Z
## 27  6191   Sc0000401    73136   69814   86271 Mcavernosa15895    T
## 28  7650   Sc0000680   151817  149039  155842 Mcavernosa18111    S
## 29  7661   Sc0000682   137909  127400  138441 Mcavernosa18143    S
## 30  7689   Sc0000691    93534   87294   99827 Mcavernosa22890    E
## 31  8033   Sc0000844    57836   54559   62548 Mcavernosa25609    K
## 32  8116   Sc0000898    70539   69193   80640 Mcavernosa23628    S
## 33  8117   Sc0000898    70540   69193   80640 Mcavernosa23628    S
## 34  8390   Sc0001344    10967    5417   11093 Mcavernosa35036    A
## 35  8855 xfSc0000031    98049   66537  100795 Mcavernosa26565    O
## 36  9465 xpSc0004679    77832   74393   86485 Mcavernosa32339    S
## 37  9722 xpSc0004753    68945   44063   78897 Mcavernosa24038    S
## 38  9723 xpSc0004753    68948   44063   78897 Mcavernosa24038    S
## 39  9745 xpSc0004768    13647   11940   16882 Mcavernosa24254    O
##                                                                                                        protein
## 1                                                                          Protein inhibitor of activated STAT
## 2                                                                                                synaptotagmin
## 3                                                                                        TRAF-type zinc finger
## 4                                                                                          Leucine Rich Repeat
## 5                                                                                              forkhead box L2
## 6                                                                                            Guanylate cyclase
## 7                                                                  Tubulin tyrosine ligase-like family, member
## 8                                                          intraflagellar transport 20 homolog (Chlamydomonas)
## 9                                                                                                       Globin
## 10                                                                                        Lectin C-type domain
## 11 Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis (By similarity)
## 12 Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis (By similarity)
## 13                                                                                           Iroquois homeobox
## 14                                                                          Diphthamide biosynthesis protein 3
## 15                                                    leucine rich repeat and sterile alpha motif containing 1
## 16                                                               ATP-binding cassette sub-family A ABC1 member
## 17                                     Microtubule associated monoxygenase, calponin and LIM domain containing
## 18                                                                              EF-hand calcium binding domain
## 19                                 pleckstrin homology domain containing, family G (with RhoGef domain) member
## 20                                                                                      Zinc finger, C2H2 type
## 21                                                                                      Lowdensity lipoprotein
## 22                                                                               armadillo repeat containing 2
## 23                                                                         chromosome 11 open reading frame 65
## 24                                                                                           hephaestin-like 1
## 25                                                                                   Transmembrane protein 205
## 26                                                                                                dystrobrevin
## 27                                                                                                  calmodulin
## 28                                                                                TBC1 domain family, member 7
## 29                                                                  nucleolar and spindle associated protein 1
## 30                                                                                            Carboxypeptidase
## 31                                                                                                UNC homeobox
## 32                                                                       BRO1 domain and CAAX motif containing
## 33                                                                       BRO1 domain and CAAX motif containing
## 34                                                                            wilms tumor 1 associated protein
## 35                                                      ADAM metallopeptidase with thrombospondin type 1 motif
## 36                                                                                               storkhead box
## 37                                                                        Chromosome 14 open reading frame 159
## 38                                                                        Chromosome 14 open reading frame 159
## 39                                                     ADAM metallopeptidase with thrombospondin type 1, motif
df_uniq <- unique(highOutsAnno$locus)
length(df_uniq)
## [1] 36
write.csv(x=highOutsAnno, file="annotedSignificantOutliers.csv")